Center for Cognitive Neuroscience - User contributions [en]

Hoffman2:FSL

2026-05-05T18:15:48Z

Hwang: /* Known Issue in Hoffman */

[[Hoffman2|Back to all things Hoffman2]]

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.

Multiple versions are maintained on the Hoffman2 cluster to allow researchers to be consistent in using the same version for data analysis within a single study. You can either:
* do nothing, and always use the "current" version of FSL on the cluster
* [[Hoffman2:Modules#FSL|actively choose]] which version of FSL you would like to run
We recommend the latter for data integrity and reproducibility.

==FSL GUI==
Make sure you source the FMRI Path in your [[Hoffman2:Profile | Profile]] before doing anything, or else you won't be able to access FSL.

To run FSL using a GUI on hoffman2, use the following command:
$ fsl &

If you received this message while opening FSL
DISPLAY is not set. Please set your DISPLAY environment variable!

It means you did not open X11 along with your ssh connection. See [[Hoffman2:Accessing_the_Cluster#GUI-Enabled_SSH_.5BRecommended.5D | here]] for more information.

==FSL TOOLS==
A complete list of tools can be found [http://www.fmrib.ox.ac.uk/fsl/fsl/list.html here]

Functional MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fabber/index.html fabber]
| Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.
|}

Structural MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/bet2/index.html bet]
| Brain Extraction Tool - segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fast4/index.html fast]
| FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| FMRIB's Integrated Registration and Segmentation Tool. FIRST uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.
|}

GUI Commands/Tools [Make sure to have X11 forwarding on]
{| class="wikitable"
|-
! Tool
! Explanation
|-
| fsl
| Bring you to the FSL menu where you can choose what type of analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography, including crossing-fibre modelling.
|-
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/featquery.html Featquery]
| A program which allows you to interrogate FEAT results by defining a mask or set of co-ordinates (in standard-space, highres-space or loweres-space) and get mean stats values and time-series.
|-
| Glm
| A GUI for setting up just the design matrix and contrasts, in the same way as in FEAT, for use with other modelling/inference programs such as randomise.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html Melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
| Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence..
|-
| Renderhighres
| Transforms all thresholded stats images in a FEAT directory into high resolution or standard space and overlays these onto the high resolution or standard space images. This then produces PNG format pictures of the overlays and, by default, deletes the 3D AVW colour overlay images.
|-
| [http://www.fmrib.ox.ac.uk/fsl/miscvis/index.html Renderstats]
| This tool allows you to combine a background image (raw FMRI or high resolution MRI) image with one or two statistics images. The statistics image(s) must be in registration with the background image.
|-
| [http://www.fmrib.ox.ac.uk/fsl/susan/index.html Susan]
| Nonlinear noise reduction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fslview/index.html fslview]
| Interactive display tool for 3D and 4D data.
|}

==Cluster==
{| class="wikitable"
|-
! Scripts that self-submit
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| [http://www.fmrib.ox.ac.uk/fsl/fslvbm/index.html fslval]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html possom]
| [http://www.fmrib.ox.ac.uk/fsl/randomise/index.html randomise]
| [http://www.fmrib.ox.ac.uk/fsl/tbss/index.html tbss]
|-
! GUIs that self-submit
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
|-
|-
|-
|}

FSL_SUB




==NO_FSL_JOBS==
Sometimes FSL doesn't know how to allocate enough resources for its jobs properly. Specifically we have found the FEAT tool often unable to do this for group analyses or other complex tasks. So we did some tinkering with FSL to allow you to override its job submission on Hoffman2 and run it like it was just on your laptop. '''The trick is to set <code>NO_FSL_JOBS=true</code> in your environment and FSL will not submit jobs.'''

===Interactive Session===
If you want to watch FEAT run (kinda like paint drying, but to each their own), you can do the following
#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line|SSH]] into the cluster
#Check out an [[Hoffman2:Interactive_Sessions|interactive node]] with the necessary time and memory
#*<code>qrsh -l h_rt=3:00:00,h_data=4G</code>
#Set the environment variable
#*<code>export NO_FSL_JOBS=true</code>
#Run your FSL commands. '''This means not using qsub, or command files, but simply executing the FSL command'''
#The commands will just run and not submit any jobs.

===Submitting a Job===
If you don't want to watch FEAT run (why would you?), you can do the following

Create a shell script (e.g. myshellscript.sh) with the following contents
#!/bin/bash
export NO_FSL_JOBS=true
feat design.fsf
# any other FSL commands you want

And make sure to run <code>chmod 750</code> to make the script executable
chmod 750 myshellscript.sh

Submit the shell script [[Hoffman2:Submitting_Jobs|as a job]] but with the adequate time and memory allocations
qsub -l h_rt=23:00:00,h_data=4G -V -m bea -cwd /path/to/myshellscript.sh

And the FSL commands will be sent into the queue to run with your time and memory constraints rather than FSL's. This may take some playing with to get the time and memory allocations correct, but at least you have the ability to tweak them.

==FSL GPU==

Some FSL tools, like ''eddy'' and ''bedpostx'', can utilize Hofmman's GPU architecture to speed up their processing times. Below is an example of how to request a CUDA 9.1-enabled GPU node.

# request Tesla P4 GPU node
qrsh -l gpu,P4,h_rt=5:00:00

module load cuda/9.1
module load fsl/6.0.4
export NO_FSL_JOBS=true

# now run eddy_cuda9.1 or bedpostx_gpu

== Known Issue in Hoffman==

When using noMachine with newer version (6.0.7.x) of FSL, user might get errors as the following

"Unable to contact" settings server : Failed to connect to socket /tmp/dbus-xxxxx: Connection refused

This is because these versions of FSL overwrite the path to the dbus and noMachine cannot find the dbus in Hoffman.

Normally dbus-launch should be under /usr/bin. If it's not, then it won't work. By checking the dbu-launch path, it can be decided if it's the same issue or not.

which dbus-launch
/usr/bin/dbus-launch

Solution:

1. check your ~/.bashrc or ~/.bash_profile, if there's any "module load FSL", comment them out.

2. Start noMachine

3. In noMachine terminal, input "module load fsl/versionxxx". Then it should avoid the same error this time.

==External Links==
* Official FSL website http://www.fmrib.ox.ac.uk/fsl/

Hoffman2:FSL

2026-05-05T18:14:04Z

Hwang: /* Known Issue in Hoffman */

[[Hoffman2|Back to all things Hoffman2]]

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.

Multiple versions are maintained on the Hoffman2 cluster to allow researchers to be consistent in using the same version for data analysis within a single study. You can either:
* do nothing, and always use the "current" version of FSL on the cluster
* [[Hoffman2:Modules#FSL|actively choose]] which version of FSL you would like to run
We recommend the latter for data integrity and reproducibility.

==FSL GUI==
Make sure you source the FMRI Path in your [[Hoffman2:Profile | Profile]] before doing anything, or else you won't be able to access FSL.

To run FSL using a GUI on hoffman2, use the following command:
$ fsl &

If you received this message while opening FSL
DISPLAY is not set. Please set your DISPLAY environment variable!

It means you did not open X11 along with your ssh connection. See [[Hoffman2:Accessing_the_Cluster#GUI-Enabled_SSH_.5BRecommended.5D | here]] for more information.

==FSL TOOLS==
A complete list of tools can be found [http://www.fmrib.ox.ac.uk/fsl/fsl/list.html here]

Functional MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fabber/index.html fabber]
| Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.
|}

Structural MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/bet2/index.html bet]
| Brain Extraction Tool - segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fast4/index.html fast]
| FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| FMRIB's Integrated Registration and Segmentation Tool. FIRST uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.
|}

GUI Commands/Tools [Make sure to have X11 forwarding on]
{| class="wikitable"
|-
! Tool
! Explanation
|-
| fsl
| Bring you to the FSL menu where you can choose what type of analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography, including crossing-fibre modelling.
|-
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/featquery.html Featquery]
| A program which allows you to interrogate FEAT results by defining a mask or set of co-ordinates (in standard-space, highres-space or loweres-space) and get mean stats values and time-series.
|-
| Glm
| A GUI for setting up just the design matrix and contrasts, in the same way as in FEAT, for use with other modelling/inference programs such as randomise.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html Melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
| Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence..
|-
| Renderhighres
| Transforms all thresholded stats images in a FEAT directory into high resolution or standard space and overlays these onto the high resolution or standard space images. This then produces PNG format pictures of the overlays and, by default, deletes the 3D AVW colour overlay images.
|-
| [http://www.fmrib.ox.ac.uk/fsl/miscvis/index.html Renderstats]
| This tool allows you to combine a background image (raw FMRI or high resolution MRI) image with one or two statistics images. The statistics image(s) must be in registration with the background image.
|-
| [http://www.fmrib.ox.ac.uk/fsl/susan/index.html Susan]
| Nonlinear noise reduction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fslview/index.html fslview]
| Interactive display tool for 3D and 4D data.
|}

==Cluster==
{| class="wikitable"
|-
! Scripts that self-submit
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| [http://www.fmrib.ox.ac.uk/fsl/fslvbm/index.html fslval]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html possom]
| [http://www.fmrib.ox.ac.uk/fsl/randomise/index.html randomise]
| [http://www.fmrib.ox.ac.uk/fsl/tbss/index.html tbss]
|-
! GUIs that self-submit
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
|-
|-
|-
|}

FSL_SUB




==NO_FSL_JOBS==
Sometimes FSL doesn't know how to allocate enough resources for its jobs properly. Specifically we have found the FEAT tool often unable to do this for group analyses or other complex tasks. So we did some tinkering with FSL to allow you to override its job submission on Hoffman2 and run it like it was just on your laptop. '''The trick is to set <code>NO_FSL_JOBS=true</code> in your environment and FSL will not submit jobs.'''

===Interactive Session===
If you want to watch FEAT run (kinda like paint drying, but to each their own), you can do the following
#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line|SSH]] into the cluster
#Check out an [[Hoffman2:Interactive_Sessions|interactive node]] with the necessary time and memory
#*<code>qrsh -l h_rt=3:00:00,h_data=4G</code>
#Set the environment variable
#*<code>export NO_FSL_JOBS=true</code>
#Run your FSL commands. '''This means not using qsub, or command files, but simply executing the FSL command'''
#The commands will just run and not submit any jobs.

===Submitting a Job===
If you don't want to watch FEAT run (why would you?), you can do the following

Create a shell script (e.g. myshellscript.sh) with the following contents
#!/bin/bash
export NO_FSL_JOBS=true
feat design.fsf
# any other FSL commands you want

And make sure to run <code>chmod 750</code> to make the script executable
chmod 750 myshellscript.sh

Submit the shell script [[Hoffman2:Submitting_Jobs|as a job]] but with the adequate time and memory allocations
qsub -l h_rt=23:00:00,h_data=4G -V -m bea -cwd /path/to/myshellscript.sh

And the FSL commands will be sent into the queue to run with your time and memory constraints rather than FSL's. This may take some playing with to get the time and memory allocations correct, but at least you have the ability to tweak them.

==FSL GPU==

Some FSL tools, like ''eddy'' and ''bedpostx'', can utilize Hofmman's GPU architecture to speed up their processing times. Below is an example of how to request a CUDA 9.1-enabled GPU node.

# request Tesla P4 GPU node
qrsh -l gpu,P4,h_rt=5:00:00

module load cuda/9.1
module load fsl/6.0.4
export NO_FSL_JOBS=true

# now run eddy_cuda9.1 or bedpostx_gpu

== Known Issue in Hoffman==

When using noMachine with newer version (6.0.7.x) of FSL, user might get errors as the following

"Unable to contact" settings server : Failed to connect to socket /tmp/dbus-xxxxx: Connection refused

This is because these versions of FSL overwrite the path to the dbus and noMachine cannot find the dbus in Hoffman.

Normally dbus-launch should be under /usr/bin. If it's not, then it won't work.

which dbus-launch
/usr/bin/dbus-launch

Solution:

1. check your ~/.bashrc or ~/.bash_profile, if there's any "module load FSL", comment them out.

2. Start noMachine

3. In noMachine terminal, input "module load fsl/versionxxx". Then it should avoid the same error this time.

==External Links==
* Official FSL website http://www.fmrib.ox.ac.uk/fsl/

Hoffman2:FSL

2026-05-05T18:10:51Z

Hwang: /* Known Issue in Hoffman */

[[Hoffman2|Back to all things Hoffman2]]

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.

Multiple versions are maintained on the Hoffman2 cluster to allow researchers to be consistent in using the same version for data analysis within a single study. You can either:
* do nothing, and always use the "current" version of FSL on the cluster
* [[Hoffman2:Modules#FSL|actively choose]] which version of FSL you would like to run
We recommend the latter for data integrity and reproducibility.

==FSL GUI==
Make sure you source the FMRI Path in your [[Hoffman2:Profile | Profile]] before doing anything, or else you won't be able to access FSL.

To run FSL using a GUI on hoffman2, use the following command:
$ fsl &

If you received this message while opening FSL
DISPLAY is not set. Please set your DISPLAY environment variable!

It means you did not open X11 along with your ssh connection. See [[Hoffman2:Accessing_the_Cluster#GUI-Enabled_SSH_.5BRecommended.5D | here]] for more information.

==FSL TOOLS==
A complete list of tools can be found [http://www.fmrib.ox.ac.uk/fsl/fsl/list.html here]

Functional MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fabber/index.html fabber]
| Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.
|}

Structural MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/bet2/index.html bet]
| Brain Extraction Tool - segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fast4/index.html fast]
| FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| FMRIB's Integrated Registration and Segmentation Tool. FIRST uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.
|}

GUI Commands/Tools [Make sure to have X11 forwarding on]
{| class="wikitable"
|-
! Tool
! Explanation
|-
| fsl
| Bring you to the FSL menu where you can choose what type of analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography, including crossing-fibre modelling.
|-
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/featquery.html Featquery]
| A program which allows you to interrogate FEAT results by defining a mask or set of co-ordinates (in standard-space, highres-space or loweres-space) and get mean stats values and time-series.
|-
| Glm
| A GUI for setting up just the design matrix and contrasts, in the same way as in FEAT, for use with other modelling/inference programs such as randomise.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html Melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
| Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence..
|-
| Renderhighres
| Transforms all thresholded stats images in a FEAT directory into high resolution or standard space and overlays these onto the high resolution or standard space images. This then produces PNG format pictures of the overlays and, by default, deletes the 3D AVW colour overlay images.
|-
| [http://www.fmrib.ox.ac.uk/fsl/miscvis/index.html Renderstats]
| This tool allows you to combine a background image (raw FMRI or high resolution MRI) image with one or two statistics images. The statistics image(s) must be in registration with the background image.
|-
| [http://www.fmrib.ox.ac.uk/fsl/susan/index.html Susan]
| Nonlinear noise reduction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fslview/index.html fslview]
| Interactive display tool for 3D and 4D data.
|}

==Cluster==
{| class="wikitable"
|-
! Scripts that self-submit
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| [http://www.fmrib.ox.ac.uk/fsl/fslvbm/index.html fslval]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html possom]
| [http://www.fmrib.ox.ac.uk/fsl/randomise/index.html randomise]
| [http://www.fmrib.ox.ac.uk/fsl/tbss/index.html tbss]
|-
! GUIs that self-submit
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
|-
|-
|-
|}

FSL_SUB




==NO_FSL_JOBS==
Sometimes FSL doesn't know how to allocate enough resources for its jobs properly. Specifically we have found the FEAT tool often unable to do this for group analyses or other complex tasks. So we did some tinkering with FSL to allow you to override its job submission on Hoffman2 and run it like it was just on your laptop. '''The trick is to set <code>NO_FSL_JOBS=true</code> in your environment and FSL will not submit jobs.'''

===Interactive Session===
If you want to watch FEAT run (kinda like paint drying, but to each their own), you can do the following
#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line|SSH]] into the cluster
#Check out an [[Hoffman2:Interactive_Sessions|interactive node]] with the necessary time and memory
#*<code>qrsh -l h_rt=3:00:00,h_data=4G</code>
#Set the environment variable
#*<code>export NO_FSL_JOBS=true</code>
#Run your FSL commands. '''This means not using qsub, or command files, but simply executing the FSL command'''
#The commands will just run and not submit any jobs.

===Submitting a Job===
If you don't want to watch FEAT run (why would you?), you can do the following

Create a shell script (e.g. myshellscript.sh) with the following contents
#!/bin/bash
export NO_FSL_JOBS=true
feat design.fsf
# any other FSL commands you want

And make sure to run <code>chmod 750</code> to make the script executable
chmod 750 myshellscript.sh

Submit the shell script [[Hoffman2:Submitting_Jobs|as a job]] but with the adequate time and memory allocations
qsub -l h_rt=23:00:00,h_data=4G -V -m bea -cwd /path/to/myshellscript.sh

And the FSL commands will be sent into the queue to run with your time and memory constraints rather than FSL's. This may take some playing with to get the time and memory allocations correct, but at least you have the ability to tweak them.

==FSL GPU==

Some FSL tools, like ''eddy'' and ''bedpostx'', can utilize Hofmman's GPU architecture to speed up their processing times. Below is an example of how to request a CUDA 9.1-enabled GPU node.

# request Tesla P4 GPU node
qrsh -l gpu,P4,h_rt=5:00:00

module load cuda/9.1
module load fsl/6.0.4
export NO_FSL_JOBS=true

# now run eddy_cuda9.1 or bedpostx_gpu

== Known Issue in Hoffman==

When using noMachine with newer version of FSL, user might get errors as the following

"Unable to contact" settings server : Failed to connect to socket /tmp/dbus-xxxxx: Connection refused

This is because these versions of FSL overwrite the path to the dbus and noMachine cannot find the dbus in Hoffman.

Normally dbus-launch should be under /usr/bin. If it's not, then it won't work.

which dbus-launch
/usr/bin/dbus-launch

Solution:

1. check your ~/.bashrc or ~/.bash_profile, if there's any "module load FSL", comment them out.

2. Start noMachine

3. In noMachine terminal, input "module load fsl/versionxxx". Then it should avoid the same error this time.

==External Links==
* Official FSL website http://www.fmrib.ox.ac.uk/fsl/

Hoffman2:FSL

2026-05-05T18:08:11Z

Hwang: /* FSL Known Issue in Hoffman */

[[Hoffman2|Back to all things Hoffman2]]

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.

Multiple versions are maintained on the Hoffman2 cluster to allow researchers to be consistent in using the same version for data analysis within a single study. You can either:
* do nothing, and always use the "current" version of FSL on the cluster
* [[Hoffman2:Modules#FSL|actively choose]] which version of FSL you would like to run
We recommend the latter for data integrity and reproducibility.

==FSL GUI==
Make sure you source the FMRI Path in your [[Hoffman2:Profile | Profile]] before doing anything, or else you won't be able to access FSL.

To run FSL using a GUI on hoffman2, use the following command:
$ fsl &

If you received this message while opening FSL
DISPLAY is not set. Please set your DISPLAY environment variable!

It means you did not open X11 along with your ssh connection. See [[Hoffman2:Accessing_the_Cluster#GUI-Enabled_SSH_.5BRecommended.5D | here]] for more information.

==FSL TOOLS==
A complete list of tools can be found [http://www.fmrib.ox.ac.uk/fsl/fsl/list.html here]

Functional MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fabber/index.html fabber]
| Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.
|}

Structural MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/bet2/index.html bet]
| Brain Extraction Tool - segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fast4/index.html fast]
| FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| FMRIB's Integrated Registration and Segmentation Tool. FIRST uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.
|}

GUI Commands/Tools [Make sure to have X11 forwarding on]
{| class="wikitable"
|-
! Tool
! Explanation
|-
| fsl
| Bring you to the FSL menu where you can choose what type of analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography, including crossing-fibre modelling.
|-
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/featquery.html Featquery]
| A program which allows you to interrogate FEAT results by defining a mask or set of co-ordinates (in standard-space, highres-space or loweres-space) and get mean stats values and time-series.
|-
| Glm
| A GUI for setting up just the design matrix and contrasts, in the same way as in FEAT, for use with other modelling/inference programs such as randomise.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html Melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
| Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence..
|-
| Renderhighres
| Transforms all thresholded stats images in a FEAT directory into high resolution or standard space and overlays these onto the high resolution or standard space images. This then produces PNG format pictures of the overlays and, by default, deletes the 3D AVW colour overlay images.
|-
| [http://www.fmrib.ox.ac.uk/fsl/miscvis/index.html Renderstats]
| This tool allows you to combine a background image (raw FMRI or high resolution MRI) image with one or two statistics images. The statistics image(s) must be in registration with the background image.
|-
| [http://www.fmrib.ox.ac.uk/fsl/susan/index.html Susan]
| Nonlinear noise reduction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fslview/index.html fslview]
| Interactive display tool for 3D and 4D data.
|}

==Cluster==
{| class="wikitable"
|-
! Scripts that self-submit
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| [http://www.fmrib.ox.ac.uk/fsl/fslvbm/index.html fslval]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html possom]
| [http://www.fmrib.ox.ac.uk/fsl/randomise/index.html randomise]
| [http://www.fmrib.ox.ac.uk/fsl/tbss/index.html tbss]
|-
! GUIs that self-submit
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
|-
|-
|-
|}

FSL_SUB




==NO_FSL_JOBS==
Sometimes FSL doesn't know how to allocate enough resources for its jobs properly. Specifically we have found the FEAT tool often unable to do this for group analyses or other complex tasks. So we did some tinkering with FSL to allow you to override its job submission on Hoffman2 and run it like it was just on your laptop. '''The trick is to set <code>NO_FSL_JOBS=true</code> in your environment and FSL will not submit jobs.'''

===Interactive Session===
If you want to watch FEAT run (kinda like paint drying, but to each their own), you can do the following
#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line|SSH]] into the cluster
#Check out an [[Hoffman2:Interactive_Sessions|interactive node]] with the necessary time and memory
#*<code>qrsh -l h_rt=3:00:00,h_data=4G</code>
#Set the environment variable
#*<code>export NO_FSL_JOBS=true</code>
#Run your FSL commands. '''This means not using qsub, or command files, but simply executing the FSL command'''
#The commands will just run and not submit any jobs.

===Submitting a Job===
If you don't want to watch FEAT run (why would you?), you can do the following

Create a shell script (e.g. myshellscript.sh) with the following contents
#!/bin/bash
export NO_FSL_JOBS=true
feat design.fsf
# any other FSL commands you want

And make sure to run <code>chmod 750</code> to make the script executable
chmod 750 myshellscript.sh

Submit the shell script [[Hoffman2:Submitting_Jobs|as a job]] but with the adequate time and memory allocations
qsub -l h_rt=23:00:00,h_data=4G -V -m bea -cwd /path/to/myshellscript.sh

And the FSL commands will be sent into the queue to run with your time and memory constraints rather than FSL's. This may take some playing with to get the time and memory allocations correct, but at least you have the ability to tweak them.

==FSL GPU==

Some FSL tools, like ''eddy'' and ''bedpostx'', can utilize Hofmman's GPU architecture to speed up their processing times. Below is an example of how to request a CUDA 9.1-enabled GPU node.

# request Tesla P4 GPU node
qrsh -l gpu,P4,h_rt=5:00:00

module load cuda/9.1
module load fsl/6.0.4
export NO_FSL_JOBS=true

# now run eddy_cuda9.1 or bedpostx_gpu

== Known Issue in Hoffman==

When using noMachine + newer version of FSL, user might get errors as the following

"Unable to contact" settings server : Failed to connect to socket /tmp/dbus-xxxxx: Connection refused

This is because these versions of FSL overwrite the path to the dbus and noMachine cannot find the dbus in Hoffman.

Normally dbus-launch should be under /usr/bin. If it's not, then it won't work.

which dbus-launch
/usr/bin/dbus-launch

Solution:

1. check your ~/.bashrc or ~/.bash_profile, if there's any "module load FSL", comment them out.

2. Start noMachine

3. In noMachine terminal, input "module load fsl/versionxxx". Then it should avoid the same error this time.

==External Links==
* Official FSL website http://www.fmrib.ox.ac.uk/fsl/

Hoffman2:FSL

2026-05-05T18:06:41Z

Hwang:

[[Hoffman2|Back to all things Hoffman2]]

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.

Multiple versions are maintained on the Hoffman2 cluster to allow researchers to be consistent in using the same version for data analysis within a single study. You can either:
* do nothing, and always use the "current" version of FSL on the cluster
* [[Hoffman2:Modules#FSL|actively choose]] which version of FSL you would like to run
We recommend the latter for data integrity and reproducibility.

==FSL GUI==
Make sure you source the FMRI Path in your [[Hoffman2:Profile | Profile]] before doing anything, or else you won't be able to access FSL.

To run FSL using a GUI on hoffman2, use the following command:
$ fsl &

If you received this message while opening FSL
DISPLAY is not set. Please set your DISPLAY environment variable!

It means you did not open X11 along with your ssh connection. See [[Hoffman2:Accessing_the_Cluster#GUI-Enabled_SSH_.5BRecommended.5D | here]] for more information.

==FSL TOOLS==
A complete list of tools can be found [http://www.fmrib.ox.ac.uk/fsl/fsl/list.html here]

Functional MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fabber/index.html fabber]
| Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.
|}

Structural MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/bet2/index.html bet]
| Brain Extraction Tool - segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fast4/index.html fast]
| FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| FMRIB's Integrated Registration and Segmentation Tool. FIRST uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.
|}

GUI Commands/Tools [Make sure to have X11 forwarding on]
{| class="wikitable"
|-
! Tool
! Explanation
|-
| fsl
| Bring you to the FSL menu where you can choose what type of analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography, including crossing-fibre modelling.
|-
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/featquery.html Featquery]
| A program which allows you to interrogate FEAT results by defining a mask or set of co-ordinates (in standard-space, highres-space or loweres-space) and get mean stats values and time-series.
|-
| Glm
| A GUI for setting up just the design matrix and contrasts, in the same way as in FEAT, for use with other modelling/inference programs such as randomise.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html Melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
| Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence..
|-
| Renderhighres
| Transforms all thresholded stats images in a FEAT directory into high resolution or standard space and overlays these onto the high resolution or standard space images. This then produces PNG format pictures of the overlays and, by default, deletes the 3D AVW colour overlay images.
|-
| [http://www.fmrib.ox.ac.uk/fsl/miscvis/index.html Renderstats]
| This tool allows you to combine a background image (raw FMRI or high resolution MRI) image with one or two statistics images. The statistics image(s) must be in registration with the background image.
|-
| [http://www.fmrib.ox.ac.uk/fsl/susan/index.html Susan]
| Nonlinear noise reduction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fslview/index.html fslview]
| Interactive display tool for 3D and 4D data.
|}

==Cluster==
{| class="wikitable"
|-
! Scripts that self-submit
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| [http://www.fmrib.ox.ac.uk/fsl/fslvbm/index.html fslval]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html possom]
| [http://www.fmrib.ox.ac.uk/fsl/randomise/index.html randomise]
| [http://www.fmrib.ox.ac.uk/fsl/tbss/index.html tbss]
|-
! GUIs that self-submit
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
|-
|-
|-
|}

FSL_SUB




==NO_FSL_JOBS==
Sometimes FSL doesn't know how to allocate enough resources for its jobs properly. Specifically we have found the FEAT tool often unable to do this for group analyses or other complex tasks. So we did some tinkering with FSL to allow you to override its job submission on Hoffman2 and run it like it was just on your laptop. '''The trick is to set <code>NO_FSL_JOBS=true</code> in your environment and FSL will not submit jobs.'''

===Interactive Session===
If you want to watch FEAT run (kinda like paint drying, but to each their own), you can do the following
#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line|SSH]] into the cluster
#Check out an [[Hoffman2:Interactive_Sessions|interactive node]] with the necessary time and memory
#*<code>qrsh -l h_rt=3:00:00,h_data=4G</code>
#Set the environment variable
#*<code>export NO_FSL_JOBS=true</code>
#Run your FSL commands. '''This means not using qsub, or command files, but simply executing the FSL command'''
#The commands will just run and not submit any jobs.

===Submitting a Job===
If you don't want to watch FEAT run (why would you?), you can do the following

Create a shell script (e.g. myshellscript.sh) with the following contents
#!/bin/bash
export NO_FSL_JOBS=true
feat design.fsf
# any other FSL commands you want

And make sure to run <code>chmod 750</code> to make the script executable
chmod 750 myshellscript.sh

Submit the shell script [[Hoffman2:Submitting_Jobs|as a job]] but with the adequate time and memory allocations
qsub -l h_rt=23:00:00,h_data=4G -V -m bea -cwd /path/to/myshellscript.sh

And the FSL commands will be sent into the queue to run with your time and memory constraints rather than FSL's. This may take some playing with to get the time and memory allocations correct, but at least you have the ability to tweak them.

==FSL GPU==

Some FSL tools, like ''eddy'' and ''bedpostx'', can utilize Hofmman's GPU architecture to speed up their processing times. Below is an example of how to request a CUDA 9.1-enabled GPU node.

# request Tesla P4 GPU node
qrsh -l gpu,P4,h_rt=5:00:00

module load cuda/9.1
module load fsl/6.0.4
export NO_FSL_JOBS=true

# now run eddy_cuda9.1 or bedpostx_gpu

==FSL Known Issue in Hoffman==

When using noMachine + newer version of FSL, user might get errors as the following

"Unable to contact" settings server : Failed to connect to socket /tmp/dbus-xxxxx: Connection refused

This is because these versions of FSL overwrite the path to the dbus and noMachine cannot find the dbus in Hoffman.

Normally dbus-launch should be under /usr/bin. If it's not, then it won't work.

which dbus-launch
/usr/bin/dbus-launch

Solution:

1. check your ~/.bashrc or ~/.bash_profile, if there's any "module load FSL", comment them out.

2. Start noMachine

3. In noMachine terminal, input "module load fsl/versionxxx". Then it should avoid the same error this time.

==External Links==
* Official FSL website http://www.fmrib.ox.ac.uk/fsl/

Hoffman2:Software Tools

2026-04-08T18:45:49Z

Hwang: /* FMRIprep */

[[Hoffman2|Back to all things Hoffman2]]

There is a CCN usergroup on Hoffman2 which is maintained for groups doing Neuroimaging work at UCLA. Tools like FSL, FreeSurfer, AFNI and Nibabel are maintained for this group separate from normal Hoffman2 programs. In order to take advantage of these tools, you need to load the modules into the interactive mode or listed in your batch mode scripts.

module load appname/version

Below is a list of the available software tools. We will do our best to update it as changes are made.

*Do not load matlab and freesurfer or matlab and RStudio as it will cause errors.

==AFNI==
[http://afni.nimh.nih.gov/afni/ Official Webste]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
|20.1.00 || || New
|- class="ccn-table-odd"
|19.0.15 || 2019.02.20 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
|17.2.07 || 2017.02.07 || Default
|- class="ccn-table-odd"
|16.3.1 || 2016.11.20 ||
|- class="ccn-table-even""
|2011.12.21.1014 ||2012.03.19 ||
|}

==ANTS==
[http://stnava.github.io/ANTs/ Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
|ants-2.3.1 || || New
|- class="ccn-table-odd"
|ants-2.2.0 || 2019.03.25 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
|ants-2.1.0-redhat || 2015.01.23 || Default
|}

==ASHS==
[https://www.nitrc.org/projects/ashs| Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 20180720 || 2018.07.20 || New
|- class="ccn-table-odd"
| 2017-02 || 2017.06.08 ||
|- class="ccn-table-odd" style="background-color:#ffffcc;"
| Rev-103 || 2016.02.24 || Default
|}

==BrainSuite==
[http://brainsuite.org/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 19a || 2019.02.19 || Default
|- class="ccn-table-odd"
| 18a || ||
|- class="ccn-table-even"
| 17a || ||
|- class="ccn-table-odd"
| 15c || 2016.02.18 || No longer supported
|}

==BrainAgeR==
[https://github.com/james-cole/brainageR Official Website]
[[Hoffman2:Software Tools:BrainAgeR|Load BrainAgeR module]]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 19a || 2019.02.19 || Default
|- class="ccn-table-odd"
| 18a || ||
|- class="ccn-table-even"
| 17a || ||
|- class="ccn-table-odd"
| 15c || 2016.02.18 || No longer supported
|}

==brms==
R library [http://https://mc-stan.org/users/interfaces/brms Official Website]

[[Hoffman2:Software Tools:brms|How to load]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 2.17.0 || 2022.06.10 || Default
|}



==Caret==
[http://brainvis.wustl.edu/wiki/index.php/Caret:About Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 5.65 (2012.01.27) || 2013.07.15 || Default, not folded into the main profile
|}

==ccn_py37==
Conda virtual environment with nibabel, nilearn, pydicom, pandas, scikit-learn, scipy

[[Hoffman2:Software Tools:ccn_py37|How to load]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| 1.0 || 2021.05.24 || CentOS 7 with Conda
|}

==Chronux==
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 2.10 || 2013.02.26 || Current
|}

==CONN==
[https://web.conn-toolbox.org/ Official Website]

[[Hoffman2:Software Tools:CONN|Load CONN module]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 19.b || || New
|- class="ccn-table-odd"
| 18.b || ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 17.f || || Default
|}

==dcm2nii==
[http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 2013.06.06 || 2014.03.06 ||
|- class="ccn-table-even"
| 2011.11.11 || circa 2011 || Current
|}

==dmctk==
[https://dicom.offis.de/dcmtk.php.en Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 3.6.0 || 2017.05.17 || Current
|- class="ccn-table-even"
| 3.6.6 || 2021.02.16
|}

==DTIprep==
[https://www.nitrc.org/projects/dtiprep/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.2.4 || 2017.12.21 ||
|- class="ccn-table-even"
| 1.2.9 || 2018.03.20 || Current
|}

==DSI Studio==
[https://dsi-studio.labsolver.org/ Official Website]

===Please note DSI studio only works with NoMachine===

[[Hoffman2:Software Tools:DSI Studio|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| "Chen" Release || 2023.07.06 || Current
|}

==dmriprep==
[https://github.com/nipreps/dmriprep Official Website]

[[Hoffman2:Software Tools:dmriprep|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.4.0 || 2020.12.10 || Current
|}

==EEGLAB==
[http://sccn.ucsd.edu/eeglab/ Official Website]

[http://sccn.ucsd.edu/wiki/EEGLAB_revision_history Release Notes]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 13.1.1b || 2014.01.29 ||
|- class="ccn-table-even"
| 12.0.2.5b || 2013.11.14 ||
|- class="ccn-table-odd"
| 11.0.5.4b || 2013.11.14 ||
|- class="ccn-table-even"
| 12.0.0.0b || 2012.12.10 ||
|- class="ccn-table-odd"
| 11.0.0.0b || 2012.02.21 ||
|- class="ccn-table-even"
| 10.2.5.8b || 2012.02.21 ||
|}

==ENIGMA==
[https://www.nitrc.org/projects/dtiprep/ Official Website]

[[Hoffman2:Software Tools:Enigma|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 20210422 || 2021.04.22 || Current
|}

==ENIGMA HALFpipe==
[https://github.com/HALFpipe/HALFpipe Official Website]

[[Hoffman2:Software Tools:HALfpipe|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.1.1 || 2021.08.27 || Current
|}

==FastSurfer==
[https://github.com/Deep-MI/FastSurfer/ Official Website]

[[Hoffman2:Software Tools:FastSurfer|Usage]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 202102 || 2021.03.01 || Current
|}

==FIT==
[https://trendscenter.org/software/fit/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| FITv2.0d || 2021.01.13 ||
|- class="ccn-table-even"
| FITv2.0e || 2021.01.13 ||
|}

==FIX==
[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide Official Website]

[[Hoffman2:Software Tools:Fix|Use Fix in Hoffman]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.06.15 || 2021.12.01 ||
|}

==FMRIprep==
[https://fmriprep.readthedocs.io/en/stable/usage.html Official Website]

[[Hoffman2:Software Tools:FMRIprep|Load pre-requisite modules]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 25.1.3 ||2025.07.27 || In Apptainer
|- class="ccn-table-even"
| 24.1.1 ||2024.11.01 || In Apptainer
|- class="ccn-table-odd"
| 23.2.0 ||2024.03.12 || In Apptainer
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 23.1.3 ||2023.08.22 || Use Apptainer module
|- class="ccn-table-odd"
| 20.2.1 ||2021.05.13 || In Singularity
|- class="ccn-table-even"
| 20.2.0rc0 || ||
|- class="ccn-table-odd"
| 20.1.1 || || * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-even"
| 1.4.0 || 2019.01.11 || Default * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-odd"
| 1.3.2 || 2019.01.11 || * [[#Known_issue_2 |known Issue ]]
|}

<div id="Known_issue_2" style="display:inline;">Known issues: please see [https://github.com/nipreps/fmriprep/blob/master/.versions.json version history] </div>

==FreeSurfer==
[http://surfer.nmr.mgh.harvard.edu/ Official Website]

[http://freesurfer.net/fswiki/ReleaseNotes Release Notes]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 7.2.0 || 2021.11.29 ||
|- class="ccn-table-odd"
| 7.1.1 || 2021.02.26 ||
|- class="ccn-table-even"
| 6.0.0 || 2017.01.18 || CentOS 6 only
|}



==FSL==
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]

[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Revision History]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 6.0.4 || 2021.01.25|| new
|- class="ccn-table-odd"
| 6.0.3 || 2021.09.30||
|- class="ccn-table-even"
| 6.0.1 || 2019.03.01 ||
|- class="ccn-table-odd"
| 6.0.0 || 2018.10.23 ||
|- class="ccn-table-even"
| 5.0.11 || 2018.03.19 ||
|- class="ccn-table-odd"
| 5.0.10 || 2017.04.24 || * [[#Known_issue_1 |Known Issue ]]
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 5.0.9 || 2015.10.02 || Default
|- class="ccn-table-odd"
| 5.0.8 || 2014.12.03 ||
|- class="ccn-table-even"
| 5.0.7 || 2013.10.17 ||
|- class="ccn-table-odd"
| 5.0.6 || 2013.12.18 || (2013.12.18-2014.10.10)
|- class="ccn-table-odd"
| 4.1.9 || 2011.12.01 ||
|- class="ccn-table-even"
| 4.0.4 || circa 2008 ||
|}

<div id="Known_issue_1" style="display:inline;">Known issue: 5.0.10 fsleyes crash on x2go</div>

==FSL_MRS==
[https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/index.html# Official Website]

[https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/changelog.html Revision History]

[[Hoffman2:Software Tools:FSL_MRS|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 2.1.12 || 2023.08.22|| new

|}

==ggseg==
[https://github.com/ggseg/ggseg Official Website]

[[Hoffman2:Software Tools:ggseg|Load pre-requisite modules]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| v1.6.5.9000 || 2023.03.1 ||
|- class="ccn-table-even"
|}

* Note: ggsegExtra and ggseg3d are also available under these libraries

==gift==
[https://trendscenter.org/software/gift/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| GroupICATv4.0b || 2017.11.14 ||
|- class="ccn-table-even"
| GroupICATv4.0c || 2021.01.04 ||
|}

==gradunwarp==
[https://github.com/Washington-University/gradunwarp Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.1.0 || 2019.06.04 ||
|}

==HCP Benchwork ==
[https://www.humanconnectome.org/software/connectome-workbench Official Website]
* Note: module name: hcp
[[Hoffman2:Software Tools:HCPBench|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 1.3.2 || 2019.05.22 || New
|- class="ccn-table-odd"
| 1.2.3 || 2018.02.13 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 1.1.1 || 2016.02.18 || Default
|- class="ccn-table-odd"
| 1.0 || ||
|- class="ccn-table-even"
| 0.84 || ||
|}

==ICA-AROMA==

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 0.4.5 || || New
|- class="ccn-table-odd" style="background-color:#ffffcc;"
| 0.4.1-beta || || Default
|}

* Note: Python 2.7 available for v0.4.5, module name: ica-aroma_py27.
[[Hoffman2:Software Tools:ica-aroma_py27|Load ica-aroma_py27 module]]

==ITKGray==
[http://vistalab.stanford.edu/newlm/index.php/ItkGray Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 080803 || 2009.11.19 || Default
|- class="ccn-table-even"
| 080128 || 2009.11.13 ||
|}

==ITKSnap==
[http://www.itksnap.org/pmwiki/pmwiki.php Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 3.4.0.QT4 || 2016.02.24 || Default
|- class="ccn-table-even"
| 3.6.0.QT4 || 2021.03.02 ||
|- class="ccn-table-odd"
| 3.8.0.QT4 || 2021.03.02 || Default
|}

==kwave==
[http://www.k-wave.org/doxygen/index.html Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 1.3 || 2020.07.20 || Current
|}

==MANGO==

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 20190905 || || Current
|}

==MRIQC==
[https://mriqc.readthedocs.io/en/latest/ Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.16.1 || 2021.03.08 || Current
|}

==NDATools==
[https://github.com/NDAR/nda-tools Official Website]

[[Hoffman2:Software Tools:NDATools|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.2.3 || 2021.03.04 || Current
|}

==OpenSmile==
[https://www.audeering.com/opensmile/ Official Website]

[[Hoffman2:Software Tools:OpenSmile|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 3.0.0 || 2021.03.23 || Current
|}

==Osprey==
[https://schorschinho.github.io/osprey/]
[[Hoffman2:Software Tools:Osprey|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 2.9.6 || 2025.03.13 || Current
|}

==Profumo==
[https://git.fmrib.ox.ac.uk/samh/profumo Official Website]

[[Hoffman2:Software Tools:Profumo|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.11.3 || 2021.06.22 || Current
|}



==RATS==
[https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 060419 || 2019.06.04 || Current
|}

==RStan==
[https://mc-stan.org/ Official Website]

[[Hoffman2:Software Tools:Rstan|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 4.1.2 || 2022.04.11 || Current
|}

==SPM==
[http://www.fil.ion.ucl.ac.uk/spm/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Last Patch Applied
! class="ccn-table-header"| Last Checked Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| SPM12-standalone || || || Current
|- class="ccn-table-even"
| SPM12 || || ||
|- class="ccn-table-odd"
| SPM8 || 5236 || 2014.01 ||
|- class="ccn-table-even"
| SPM5 || Unknown || N/A || No longer supported
|}

==TrackVis/Diffusion Toolkit==
[http://trackvis.org/ Official Website 1]

[http://trackvis.org/dtk/ Official Website 2]
{| class="wikitable"
! class="ccn-table-header"| Tool
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Last Checked Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| TrackVis || 0.5.2.2 || 2014.03.06 ||
|- class="ccn-table-even"
| Diffusion Toolkit || 0.6.2.2 || 204.03.06 ||
|}

==WEKA==
[http://www.cs.waikato.ac.nz/ml/weka/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| 3.8.1 || ||
|- class="ccn-table-odd"
| 3.7.10 || 2014.03.03 ||
|- class="ccn-table-even"
| 3.6.5 || circa 2011.08 ||
|}



==External Links==
*[https://www.hoffman2.idre.ucla.edu/software/ Other Hoffman2 Software]

Hoffman2:Software Tools

2026-04-08T18:43:43Z

Hwang: /* FMRIprep */

[[Hoffman2|Back to all things Hoffman2]]

There is a CCN usergroup on Hoffman2 which is maintained for groups doing Neuroimaging work at UCLA. Tools like FSL, FreeSurfer, AFNI and Nibabel are maintained for this group separate from normal Hoffman2 programs. In order to take advantage of these tools, you need to load the modules into the interactive mode or listed in your batch mode scripts.

module load appname/version

Below is a list of the available software tools. We will do our best to update it as changes are made.

*Do not load matlab and freesurfer or matlab and RStudio as it will cause errors.

==AFNI==
[http://afni.nimh.nih.gov/afni/ Official Webste]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
|20.1.00 || || New
|- class="ccn-table-odd"
|19.0.15 || 2019.02.20 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
|17.2.07 || 2017.02.07 || Default
|- class="ccn-table-odd"
|16.3.1 || 2016.11.20 ||
|- class="ccn-table-even""
|2011.12.21.1014 ||2012.03.19 ||
|}

==ANTS==
[http://stnava.github.io/ANTs/ Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
|ants-2.3.1 || || New
|- class="ccn-table-odd"
|ants-2.2.0 || 2019.03.25 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
|ants-2.1.0-redhat || 2015.01.23 || Default
|}

==ASHS==
[https://www.nitrc.org/projects/ashs| Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 20180720 || 2018.07.20 || New
|- class="ccn-table-odd"
| 2017-02 || 2017.06.08 ||
|- class="ccn-table-odd" style="background-color:#ffffcc;"
| Rev-103 || 2016.02.24 || Default
|}

==BrainSuite==
[http://brainsuite.org/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 19a || 2019.02.19 || Default
|- class="ccn-table-odd"
| 18a || ||
|- class="ccn-table-even"
| 17a || ||
|- class="ccn-table-odd"
| 15c || 2016.02.18 || No longer supported
|}

==BrainAgeR==
[https://github.com/james-cole/brainageR Official Website]
[[Hoffman2:Software Tools:BrainAgeR|Load BrainAgeR module]]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 19a || 2019.02.19 || Default
|- class="ccn-table-odd"
| 18a || ||
|- class="ccn-table-even"
| 17a || ||
|- class="ccn-table-odd"
| 15c || 2016.02.18 || No longer supported
|}

==brms==
R library [http://https://mc-stan.org/users/interfaces/brms Official Website]

[[Hoffman2:Software Tools:brms|How to load]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 2.17.0 || 2022.06.10 || Default
|}



==Caret==
[http://brainvis.wustl.edu/wiki/index.php/Caret:About Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 5.65 (2012.01.27) || 2013.07.15 || Default, not folded into the main profile
|}

==ccn_py37==
Conda virtual environment with nibabel, nilearn, pydicom, pandas, scikit-learn, scipy

[[Hoffman2:Software Tools:ccn_py37|How to load]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| 1.0 || 2021.05.24 || CentOS 7 with Conda
|}

==Chronux==
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 2.10 || 2013.02.26 || Current
|}

==CONN==
[https://web.conn-toolbox.org/ Official Website]

[[Hoffman2:Software Tools:CONN|Load CONN module]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 19.b || || New
|- class="ccn-table-odd"
| 18.b || ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 17.f || || Default
|}

==dcm2nii==
[http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 2013.06.06 || 2014.03.06 ||
|- class="ccn-table-even"
| 2011.11.11 || circa 2011 || Current
|}

==dmctk==
[https://dicom.offis.de/dcmtk.php.en Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 3.6.0 || 2017.05.17 || Current
|- class="ccn-table-even"
| 3.6.6 || 2021.02.16
|}

==DTIprep==
[https://www.nitrc.org/projects/dtiprep/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.2.4 || 2017.12.21 ||
|- class="ccn-table-even"
| 1.2.9 || 2018.03.20 || Current
|}

==DSI Studio==
[https://dsi-studio.labsolver.org/ Official Website]

===Please note DSI studio only works with NoMachine===

[[Hoffman2:Software Tools:DSI Studio|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| "Chen" Release || 2023.07.06 || Current
|}

==dmriprep==
[https://github.com/nipreps/dmriprep Official Website]

[[Hoffman2:Software Tools:dmriprep|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.4.0 || 2020.12.10 || Current
|}

==EEGLAB==
[http://sccn.ucsd.edu/eeglab/ Official Website]

[http://sccn.ucsd.edu/wiki/EEGLAB_revision_history Release Notes]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 13.1.1b || 2014.01.29 ||
|- class="ccn-table-even"
| 12.0.2.5b || 2013.11.14 ||
|- class="ccn-table-odd"
| 11.0.5.4b || 2013.11.14 ||
|- class="ccn-table-even"
| 12.0.0.0b || 2012.12.10 ||
|- class="ccn-table-odd"
| 11.0.0.0b || 2012.02.21 ||
|- class="ccn-table-even"
| 10.2.5.8b || 2012.02.21 ||
|}

==ENIGMA==
[https://www.nitrc.org/projects/dtiprep/ Official Website]

[[Hoffman2:Software Tools:Enigma|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 20210422 || 2021.04.22 || Current
|}

==ENIGMA HALFpipe==
[https://github.com/HALFpipe/HALFpipe Official Website]

[[Hoffman2:Software Tools:HALfpipe|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.1.1 || 2021.08.27 || Current
|}

==FastSurfer==
[https://github.com/Deep-MI/FastSurfer/ Official Website]

[[Hoffman2:Software Tools:FastSurfer|Usage]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 202102 || 2021.03.01 || Current
|}

==FIT==
[https://trendscenter.org/software/fit/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| FITv2.0d || 2021.01.13 ||
|- class="ccn-table-even"
| FITv2.0e || 2021.01.13 ||
|}

==FIX==
[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide Official Website]

[[Hoffman2:Software Tools:Fix|Use Fix in Hoffman]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.06.15 || 2021.12.01 ||
|}

==FMRIprep==
[https://fmriprep.readthedocs.io/en/stable/usage.html Official Website]

[[Hoffman2:Software Tools:FMRIprep|Load pre-requisite modules]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 23.2.0 ||2023.05.13 || In Apptainer
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 23.1.3 ||2023.08.22 || Use Apptainer module
|- class="ccn-table-odd"
| 20.2.1 ||2021.05.13 || In Singularity
|- class="ccn-table-even"
| 20.2.0rc0 || ||
|- class="ccn-table-odd"
| 20.1.1 || || * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-even"
| 1.4.0 || 2019.01.11 || Default * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-odd"
| 1.3.2 || 2019.01.11 || * [[#Known_issue_2 |known Issue ]]
|}

<div id="Known_issue_2" style="display:inline;">Known issues: please see [https://github.com/nipreps/fmriprep/blob/master/.versions.json version history] </div>

==FreeSurfer==
[http://surfer.nmr.mgh.harvard.edu/ Official Website]

[http://freesurfer.net/fswiki/ReleaseNotes Release Notes]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 7.2.0 || 2021.11.29 ||
|- class="ccn-table-odd"
| 7.1.1 || 2021.02.26 ||
|- class="ccn-table-even"
| 6.0.0 || 2017.01.18 || CentOS 6 only
|}



==FSL==
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]

[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Revision History]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 6.0.4 || 2021.01.25|| new
|- class="ccn-table-odd"
| 6.0.3 || 2021.09.30||
|- class="ccn-table-even"
| 6.0.1 || 2019.03.01 ||
|- class="ccn-table-odd"
| 6.0.0 || 2018.10.23 ||
|- class="ccn-table-even"
| 5.0.11 || 2018.03.19 ||
|- class="ccn-table-odd"
| 5.0.10 || 2017.04.24 || * [[#Known_issue_1 |Known Issue ]]
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 5.0.9 || 2015.10.02 || Default
|- class="ccn-table-odd"
| 5.0.8 || 2014.12.03 ||
|- class="ccn-table-even"
| 5.0.7 || 2013.10.17 ||
|- class="ccn-table-odd"
| 5.0.6 || 2013.12.18 || (2013.12.18-2014.10.10)
|- class="ccn-table-odd"
| 4.1.9 || 2011.12.01 ||
|- class="ccn-table-even"
| 4.0.4 || circa 2008 ||
|}

<div id="Known_issue_1" style="display:inline;">Known issue: 5.0.10 fsleyes crash on x2go</div>

==FSL_MRS==
[https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/index.html# Official Website]

[https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/changelog.html Revision History]

[[Hoffman2:Software Tools:FSL_MRS|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 2.1.12 || 2023.08.22|| new

|}

==ggseg==
[https://github.com/ggseg/ggseg Official Website]

[[Hoffman2:Software Tools:ggseg|Load pre-requisite modules]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| v1.6.5.9000 || 2023.03.1 ||
|- class="ccn-table-even"
|}

* Note: ggsegExtra and ggseg3d are also available under these libraries

==gift==
[https://trendscenter.org/software/gift/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| GroupICATv4.0b || 2017.11.14 ||
|- class="ccn-table-even"
| GroupICATv4.0c || 2021.01.04 ||
|}

==gradunwarp==
[https://github.com/Washington-University/gradunwarp Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.1.0 || 2019.06.04 ||
|}

==HCP Benchwork ==
[https://www.humanconnectome.org/software/connectome-workbench Official Website]
* Note: module name: hcp
[[Hoffman2:Software Tools:HCPBench|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 1.3.2 || 2019.05.22 || New
|- class="ccn-table-odd"
| 1.2.3 || 2018.02.13 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 1.1.1 || 2016.02.18 || Default
|- class="ccn-table-odd"
| 1.0 || ||
|- class="ccn-table-even"
| 0.84 || ||
|}

==ICA-AROMA==

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 0.4.5 || || New
|- class="ccn-table-odd" style="background-color:#ffffcc;"
| 0.4.1-beta || || Default
|}

* Note: Python 2.7 available for v0.4.5, module name: ica-aroma_py27.
[[Hoffman2:Software Tools:ica-aroma_py27|Load ica-aroma_py27 module]]

==ITKGray==
[http://vistalab.stanford.edu/newlm/index.php/ItkGray Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 080803 || 2009.11.19 || Default
|- class="ccn-table-even"
| 080128 || 2009.11.13 ||
|}

==ITKSnap==
[http://www.itksnap.org/pmwiki/pmwiki.php Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 3.4.0.QT4 || 2016.02.24 || Default
|- class="ccn-table-even"
| 3.6.0.QT4 || 2021.03.02 ||
|- class="ccn-table-odd"
| 3.8.0.QT4 || 2021.03.02 || Default
|}

==kwave==
[http://www.k-wave.org/doxygen/index.html Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 1.3 || 2020.07.20 || Current
|}

==MANGO==

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 20190905 || || Current
|}

==MRIQC==
[https://mriqc.readthedocs.io/en/latest/ Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.16.1 || 2021.03.08 || Current
|}

==NDATools==
[https://github.com/NDAR/nda-tools Official Website]

[[Hoffman2:Software Tools:NDATools|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.2.3 || 2021.03.04 || Current
|}

==OpenSmile==
[https://www.audeering.com/opensmile/ Official Website]

[[Hoffman2:Software Tools:OpenSmile|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 3.0.0 || 2021.03.23 || Current
|}

==Osprey==
[https://schorschinho.github.io/osprey/]
[[Hoffman2:Software Tools:Osprey|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 2.9.6 || 2025.03.13 || Current
|}

==Profumo==
[https://git.fmrib.ox.ac.uk/samh/profumo Official Website]

[[Hoffman2:Software Tools:Profumo|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.11.3 || 2021.06.22 || Current
|}



==RATS==
[https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 060419 || 2019.06.04 || Current
|}

==RStan==
[https://mc-stan.org/ Official Website]

[[Hoffman2:Software Tools:Rstan|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 4.1.2 || 2022.04.11 || Current
|}

==SPM==
[http://www.fil.ion.ucl.ac.uk/spm/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Last Patch Applied
! class="ccn-table-header"| Last Checked Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| SPM12-standalone || || || Current
|- class="ccn-table-even"
| SPM12 || || ||
|- class="ccn-table-odd"
| SPM8 || 5236 || 2014.01 ||
|- class="ccn-table-even"
| SPM5 || Unknown || N/A || No longer supported
|}

==TrackVis/Diffusion Toolkit==
[http://trackvis.org/ Official Website 1]

[http://trackvis.org/dtk/ Official Website 2]
{| class="wikitable"
! class="ccn-table-header"| Tool
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Last Checked Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| TrackVis || 0.5.2.2 || 2014.03.06 ||
|- class="ccn-table-even"
| Diffusion Toolkit || 0.6.2.2 || 204.03.06 ||
|}

==WEKA==
[http://www.cs.waikato.ac.nz/ml/weka/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| 3.8.1 || ||
|- class="ccn-table-odd"
| 3.7.10 || 2014.03.03 ||
|- class="ccn-table-even"
| 3.6.5 || circa 2011.08 ||
|}



==External Links==
*[https://www.hoffman2.idre.ucla.edu/software/ Other Hoffman2 Software]

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:28:55Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
-w PATH/TO/WORKSPACE \
--output-spaces SPACE_NAME \
--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
PATH/TO/DATA/DIR PATH/TO/OUTPUT/DIR \
participant --participant-label label

* Note: By default, fmriprep uses "MNI152NLin2009cAsym" space if no SPACE_NAME specified with --output-spaces option

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:28:38Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
-w PATH/TO/WORKSPACE \
--output-spaces SPACE_NAME \
--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
PATH/TO/DATA/DIR PATH/TO/OUTPUT/DIR \
participant --participant-label label

* By default, fmriprep uses "MNI152NLin2009cAsym" space if no SPACE_NAME specified with --output-spaces option

Hoffman2:Singularity

2026-04-08T18:19:45Z

Hwang: /* Singularity */

== Singularity ==

Singularity is a type of container technology. It is provided in Hoffman2 currently.

* Note: Singularity's newer versions are under its new name "Apptainer". It's recommended to use Apptainer instead of Singularity.
Just need to replace all the "singularity" with "apptainer" in the following command and it should work the same way.

===How to use Singularity===

The example code here is from IDRE team's
[https://gitlab.idre.ucla.edu/cpeterson/singularity_ws/-/tree/master | gitlab].
Please check it up for more information.

====Interactive mode ====
In a CentOs 7 Node, load Singularity module as

module load singularity
singularity shell --userns $H2_CONTAINER_LOC/tensorflow-2.4.1-gpu-jupyter.sif

Then run your command inside of the container

python3 tf-example.py > tf-example-batch.out

====Batch mode====
Add the following line into your batch job script

module load singularity/3.7.1

Use "singularity exec" to run command in Singularity container

Example

singularity exec --userns $H2_CONTAINER_LOC/tensorflow-2.4.1-gpu-jupyter.sif python3 tf-example.py > tf-example-batch.out

===Convert Docker image for Singularity===
Docker image can be converted for Singularity

export SINGULARITY_CACHEDIR=$SCRATCH/singularity_cache
singularity pull tensorflow-1.15.5-gpu-jupyter.sif docker://tensorflow/tensorflow:1.15.5-gpu-jupyter

Hoffman2:Singularity

2026-04-08T18:19:13Z

Hwang: /* Singularity */

== Singularity ==

Singularity is a type of container technology. It is provided in Hoffman2 currently.

* Note: Singularity's newer versions are changed to a new name "Apptainer". It's recommended to use Apptainer instead of Singularity.
Just need to replace all the "singularity" with "apptainer" in the following command and it should work the same way.

===How to use Singularity===

The example code here is from IDRE team's
[https://gitlab.idre.ucla.edu/cpeterson/singularity_ws/-/tree/master | gitlab].
Please check it up for more information.

====Interactive mode ====
In a CentOs 7 Node, load Singularity module as

module load singularity
singularity shell --userns $H2_CONTAINER_LOC/tensorflow-2.4.1-gpu-jupyter.sif

Then run your command inside of the container

python3 tf-example.py > tf-example-batch.out

====Batch mode====
Add the following line into your batch job script

module load singularity/3.7.1

Use "singularity exec" to run command in Singularity container

Example

singularity exec --userns $H2_CONTAINER_LOC/tensorflow-2.4.1-gpu-jupyter.sif python3 tf-example.py > tf-example-batch.out

===Convert Docker image for Singularity===
Docker image can be converted for Singularity

export SINGULARITY_CACHEDIR=$SCRATCH/singularity_cache
singularity pull tensorflow-1.15.5-gpu-jupyter.sif docker://tensorflow/tensorflow:1.15.5-gpu-jupyter

Hoffman2:Singularity

2026-04-08T18:18:57Z

Hwang:

== Singularity ==

Singularity is a type of container technology. It is provided in Hoffman2 currently.

* Note: Singularity's newer versions are changed to a new name "Apptainer". It's recommended to use Apptainer instead of Singularity.

* Just need to replace all the "singularity" with "apptainer" in the following command and it should work the same way.

===How to use Singularity===

The example code here is from IDRE team's
[https://gitlab.idre.ucla.edu/cpeterson/singularity_ws/-/tree/master | gitlab].
Please check it up for more information.

====Interactive mode ====
In a CentOs 7 Node, load Singularity module as

module load singularity
singularity shell --userns $H2_CONTAINER_LOC/tensorflow-2.4.1-gpu-jupyter.sif

Then run your command inside of the container

python3 tf-example.py > tf-example-batch.out

====Batch mode====
Add the following line into your batch job script

module load singularity/3.7.1

Use "singularity exec" to run command in Singularity container

Example

singularity exec --userns $H2_CONTAINER_LOC/tensorflow-2.4.1-gpu-jupyter.sif python3 tf-example.py > tf-example-batch.out

===Convert Docker image for Singularity===
Docker image can be converted for Singularity

export SINGULARITY_CACHEDIR=$SCRATCH/singularity_cache
singularity pull tensorflow-1.15.5-gpu-jupyter.sif docker://tensorflow/tensorflow:1.15.5-gpu-jupyter

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:16:11Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
-w path/to/workspace \
--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
path/to/data/dir path/to/output/dir \
participant --participant-label label

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:15:42Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
-w path/to/workspace \
--participant_label sub-xxxx \
--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
path/to/data/dir path/to/output/dir \
participant --participant-label label

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:15:31Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
-w path/to/workspace
--participant_label sub-xxxx \
--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
path/to/data/dir path/to/output/dir \
participant --participant-label label

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:11:56Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
--participant_label sub-xxxx
--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
path/to/data/dir path/to/output/dir \
participant --participant-label label

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:09:45Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
path/to/data/dir path/to/output/dir \
participant --participant-label label

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:07:31Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
path/to/data/dir path/to/output/dir \
participant --participant-label label

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:06:45Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/23.1.3-fmriprep.sif \
path/to/data/dir path/to/output/dir \
participant --participant-label label

Hoffman2:Software Tools:FMRIprep

2026-04-08T18:06:10Z

Hwang:

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

[https://fmriprep.org/en/stable/ Official Website]

[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

From version '''23.1.3''', FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/23.1.3-fmriprep.sif \
path/to/data/dir path/to/output/dir \
participant --participant-label label

Hoffman2 maintenance and Issues

2026-01-31T00:46:31Z

Hwang: /* Update date: 2023.04.06 */

== Issues and Solutions ==

=== Update date: 2023.04.06 ===

Trying to launch freeview results in a segmentation fault error on gpu nodes

Solution:

run on the gpu node: export __GLX_VENDOR_LIBRARY_NAME=mesa

Now launch freeview

=== Update date: 2023.01.13 ===

After launching freesurfer or RStudio one cannot launch the application and encounters:

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Solution:

Comment out any matlab modules in the bashrc or module unload bashrc and launch the application again.

=== Update date: 2022.07.05 ===

After login noMachine client, one cannot start a new session because of error message "No available session on this server"

Solution:

On Hoffman
rm -r ~/.nx

On your local machine
rm -r ~/.nx

Reconnect and this doesn't solver your problem, repeat these steps and uninstall noMachine then install it again with the most recent version.

=== Update date: 2021.12.02 ===

Some functions in FSL/6.0.4 gets "Illegal instruction" error message and fail on AMD nodes

Solution:

Request a Intel node by adding "arch=intel*" in the option, for example

qrsh -l arch=intel*,h_rt=4:00:00,h_data=8G

=== Update date: 2021.11.10 ===

IDRE team's gitlab is not responding.

For users who need to download the newer version of h2jupynb, please find it in Hoffman at

/u/project/CCN/apps/scripts/idre_scripts/h2jupynb

=== Update date: 2021.11.05 ===

I am able to login to NX1 currently. So both NX1 and NX2 are working at this point.

=== Update date: 2021.11.02 ===

NX2 is accepting new connections currently after IDRE team made some changes on the server. User can login nx1 but not able to create new sessions or connect to the old session. Requesting investigation from IDRE team.

=== Update date: 2021.11.01 ===

Unable to connect to nx1 and nx2 with noMachine. Waiting for IDRE team's reply.

=== Update date: 2021.10.19 ===

FSL 6.0.3 has been re-installed and the FSLeyes in this version is working in x2go and noMachine.

=== Update date: 2021.10.15 ===
Here's a list of the known issues after Hoffman2 maintenance

==== Known issue 1====

x2go and noMachine interface looks froze or in full screen mode, user cannot find menu bar.

'''Solution''':

If you are using GNOME as the desktop interface, please change to MATE. KDE works as well but you might have to delete the ~/.x2go and ~/.x2goclient in your local machine (with MacOS).

==== Known issue 2====

FSLeyes in FSL 6.0.4 and 6.0.3 does not load GUI on x2go and noMachine (Other versions work, as well as fslview)

'''Solution''' (for both x2go and noMachine):

For FSLeyes in FSL 6.0.4, type in the following command line after you start interactive session, and before you run fsleyes

unset LIBGL_ALWAYS_INDIRECT

For FSLeyes in FSL 6.0.3, fsleyes will be upgraded shortly to fix the current issue.

==== Known issue 3 ====

FreeView GUI opens but cannot load images successfully

'''Solution''':

In noMachine, use "unset LIBGL_ALWAYS_INDIRECT" command should fix the issue

In x2go, "unset LIBGL_ALWAYS_INDIRECT" does not seem to work all the time. We are still looking into it.

==== Known issue 4 ====

Jupyter Notebook does not open properly with IDRE's script h2jupynb

Reason: The previous version of this script which was used before the maintenance tries to load Python/3.7.1 which does not exit in CentOS 7 after the upgrade.

'''Solution''':

Download the newest h2jupynb script from IDRE's gitlab

https://gitlab.idre.ucla.edu/dauria/jupyter-notebook

==== Known issue 5 ====

Matlab GUI gives out warning messages as following

[1029/151141.170798:ERROR:gles2_cmd_decoder.cc(9632)] [.Offscreen-MainThread-0x2ac244e220f0]RENDER WARNING: texture bound to texture unit 0 is not renderable. It maybe non-power-of-2 and have incompatible texture filtering.
[1029/151204.562839:ERROR:gles2_cmd_decoder.cc(17399)] [.Offscreen-MainThread-0x2ac244e220f0]GL ERROR :GL_INVALID_OPERATION : glCreateAndConsumeTextureCHROMIUM: invalid mailbox name

'''Solution''':

Run "unset LIBGL_ALWAYS_INDIRECT" command in the terminal after you start interactive mode and before you launch Matlab GUI.

Hoffman2 maintenance and Issues

2026-01-31T00:46:17Z

Hwang: /* Update date: 2023.04.06 */

== Issues and Solutions ==

=== Update date: 2023.04.06 ===

Trying to launch freeview results in a segmentation fault error on gpu nodes

Solutions:

run on the gpu node: export __GLX_VENDOR_LIBRARY_NAME=mesa

Now launch freeview

=== Update date: 2023.01.13 ===

After launching freesurfer or RStudio one cannot launch the application and encounters:

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Solution:

Comment out any matlab modules in the bashrc or module unload bashrc and launch the application again.

=== Update date: 2022.07.05 ===

After login noMachine client, one cannot start a new session because of error message "No available session on this server"

Solution:

On Hoffman
rm -r ~/.nx

On your local machine
rm -r ~/.nx

Reconnect and this doesn't solver your problem, repeat these steps and uninstall noMachine then install it again with the most recent version.

=== Update date: 2021.12.02 ===

Some functions in FSL/6.0.4 gets "Illegal instruction" error message and fail on AMD nodes

Solution:

Request a Intel node by adding "arch=intel*" in the option, for example

qrsh -l arch=intel*,h_rt=4:00:00,h_data=8G

=== Update date: 2021.11.10 ===

IDRE team's gitlab is not responding.

For users who need to download the newer version of h2jupynb, please find it in Hoffman at

/u/project/CCN/apps/scripts/idre_scripts/h2jupynb

=== Update date: 2021.11.05 ===

I am able to login to NX1 currently. So both NX1 and NX2 are working at this point.

=== Update date: 2021.11.02 ===

NX2 is accepting new connections currently after IDRE team made some changes on the server. User can login nx1 but not able to create new sessions or connect to the old session. Requesting investigation from IDRE team.

=== Update date: 2021.11.01 ===

Unable to connect to nx1 and nx2 with noMachine. Waiting for IDRE team's reply.

=== Update date: 2021.10.19 ===

FSL 6.0.3 has been re-installed and the FSLeyes in this version is working in x2go and noMachine.

=== Update date: 2021.10.15 ===
Here's a list of the known issues after Hoffman2 maintenance

==== Known issue 1====

x2go and noMachine interface looks froze or in full screen mode, user cannot find menu bar.

'''Solution''':

If you are using GNOME as the desktop interface, please change to MATE. KDE works as well but you might have to delete the ~/.x2go and ~/.x2goclient in your local machine (with MacOS).

==== Known issue 2====

FSLeyes in FSL 6.0.4 and 6.0.3 does not load GUI on x2go and noMachine (Other versions work, as well as fslview)

'''Solution''' (for both x2go and noMachine):

For FSLeyes in FSL 6.0.4, type in the following command line after you start interactive session, and before you run fsleyes

unset LIBGL_ALWAYS_INDIRECT

For FSLeyes in FSL 6.0.3, fsleyes will be upgraded shortly to fix the current issue.

==== Known issue 3 ====

FreeView GUI opens but cannot load images successfully

'''Solution''':

In noMachine, use "unset LIBGL_ALWAYS_INDIRECT" command should fix the issue

In x2go, "unset LIBGL_ALWAYS_INDIRECT" does not seem to work all the time. We are still looking into it.

==== Known issue 4 ====

Jupyter Notebook does not open properly with IDRE's script h2jupynb

Reason: The previous version of this script which was used before the maintenance tries to load Python/3.7.1 which does not exit in CentOS 7 after the upgrade.

'''Solution''':

Download the newest h2jupynb script from IDRE's gitlab

https://gitlab.idre.ucla.edu/dauria/jupyter-notebook

==== Known issue 5 ====

Matlab GUI gives out warning messages as following

[1029/151141.170798:ERROR:gles2_cmd_decoder.cc(9632)] [.Offscreen-MainThread-0x2ac244e220f0]RENDER WARNING: texture bound to texture unit 0 is not renderable. It maybe non-power-of-2 and have incompatible texture filtering.
[1029/151204.562839:ERROR:gles2_cmd_decoder.cc(17399)] [.Offscreen-MainThread-0x2ac244e220f0]GL ERROR :GL_INVALID_OPERATION : glCreateAndConsumeTextureCHROMIUM: invalid mailbox name

'''Solution''':

Run "unset LIBGL_ALWAYS_INDIRECT" command in the terminal after you start interactive mode and before you launch Matlab GUI.

Hoffman2:Scripts:setup subject 3

2025-07-02T16:58:21Z

Hwang: /* Basic Usage */

==Setup Environment==
To use this script, load the ccnscripts module first:

module load ccnscripts

==Setup_subject script usage==
Setup_subject_3 (also named as setup_subject_bids) is built on top of [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Scripts:setup_subject setup_subject_2]. The major goal is to apply BIDs format on the data structure. Besides of using BIDs structure, it added other useful features as well.

Setup_subject_3 has all the functions which exist in setup_subject_2 and works the same way with the same options as setup_subject_2.

===Recent updates===

* Change participant.tsv to participants.tsv

* Change default of mprage to be skipped

* Add TaskName field to Json files of functional data

* Add default dataset_description.json file and --datadesc option

* Add --dcm2niix option

* Add --intendedfor flag for adding "intendedfor" field to FieldMap

===Basic Usage===
setup_subject_3 [option] basedir subjectID

basedir is where you want the processed data to be stored in your Hoffman account,

subjectID is the subject folder name under /Dicom/data/YOURGROUP/ in Dicom server

<pre style="color: red">Use "setup_subject_bids_xa30" collected for data after Scanner upgrade to xa30 protocol </pre>

===Options:===

====Options for both BIDs mode and non-BIDs mode====
--download hostname,userid,path
download data from Dicom server to you hoffman account
It requires 3 argument, separated by comma(,)
(If you have downloaded the data already, this option is not needed)

1. hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server).
2. userid: Your Dicom server user ID
3. path: path to the subject data in dicom server (/Dicom/data/YOURGROUP)

-d (or --do) : use this option to specify the processing you want to add
After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: submit the job in batch mode

(Using option diags requires mcflirt, bet and melodic to be processed first)

-s (or --skip)
this option to specify the processing you want to skip
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_3 script

--spm
Set SPM compatibility

====Options for BIDs mode only====
--bids
BIDs format: specify using BIDs structure to group result files. However this option often being used with --config option to choose configuration file.
Without configuration file, the name conversion might not be correct under BIDs format rule.

--config FILEPATH/FILENAME
Specifying the BIDs naming configuration file path and name. Users should generate this file based on their data and BIDSs formatting rule. Here's more about the [[BIDs configuration file]].

--sessdir ses-NN
Specify session directory name. When the subject has multiple sessions, by default the processed results will all go under sub-xxxx/[anat | func | dwi | fmap] without separation based on sessions. If you want to have all the NIfTi converted files to be located in one specific session directory, you can use this option and all files will go under sub-xxxx/ses-NN/[anat | func | dwi | fmap ] (NN represents session number, e.g. 02)

--notar
No compression of dicom/ folder. Normally raw dicom data will be compressed into dicom*.tar.gz at the end of NiFTI convert. With this option, it will not compress.
This option is good when you know you want to run the setup_subject_3 script again and want to save time on compression and decompression of the data.
You should run without this option on the last run so it will save the disk usage.

--setgrp ''GROUPNAME''
Force the data's group to be set as the GROUPNAME specified. The GROUPNAME need to be an existing valid group name in Hoffman.

--pipeline ''PIPELINE_NAME''
Specify pipeline name used for analysis ( fsl is the default value)

--dcm2niix ''DCM2NIIX_VERSION''
Specify DCM2NIIX module version. The version has to match the available mricron module version in Hoffman2.
For example, to use mricron/20200331,
--dcm2niix 20200331
To find the version list to choose from, use
module av mricron

--datadesc /path/to/your/dataset_description.json
Specify dataset_description.json file location.
If there's no dataset_description.json file in your base bids directory and this option is not used, it will copy a default simple template to the bids folder. If your base directory has dataset_description.json already, it won't be over written.
This option should have the full path to your dataset_description followed.

--intendedfor
Add "intendedfor" field to fieldmap's json file with paths to the functional data.
This option is a flag and optional for Bids format.

When this flag is on, the script will look for files under dwi/ and func/ folder and add the file paths to *_epi.json files in fmap/ folder for "intendedfor" field.

===Data Structure===

=====Non-BIDs mode=====
folder subjectID will be created under basedir the user specified.
Then Dicom Raw data will be under dicom/ folder during NiFTI convert then compressed into dicom.tar.gz
Result of NiFTI convert will be under raw/ folder

ls basedir/subjectID
analysis behav dicom notes raw

=====BIDs mode=====
basedir/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/
|_
sourcedata/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
dicom/ setup_log.xxxxxxx
|_
derivatives/
|_
PipelineName/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/

===Examples: ===

Load the script module first:
module load ccnscripts

====NON-BIDs Mode====

Download data and run NIFTI convert
setup_subject_3 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ -s mprage basedir subjectID
( /dicom/data/YOURGROUP/subjectID is the path to the raw data in Dicom server. We skip mprage here since it will be run by default)

Download data and run NIFTI convert and other FSL processing:
setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download
setup_subject_3 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject_3 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject_3 -d mprage basedir subjectID

Skip mcflirt,bet,melodic,diags
setup_subject_3 -s mcflirt,bet,melodic,diags basedir subjectID

====BIDs mode====

Download data and run debabel with Bids format, skip mprage.

setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ --bids --config ~/bidsname-sub123.conf -s mprage basedir subjectID

===Notes===
Log File: provides useful details about what commands were run, their output and the script's status. It's located at the following location for bids mode and non-bids mode

BIDs mode

basedir/sourcedata/sub-subjectID/setup_log.date_numbers

Non-BIDs mode

basedir/subjectID/notes/setup_log.date_numbers

Hoffman2:Scripts:setup subject 3

2025-07-02T16:58:04Z

Hwang: /* Basic Usage */

==Setup Environment==
To use this script, load the ccnscripts module first:

module load ccnscripts

==Setup_subject script usage==
Setup_subject_3 (also named as setup_subject_bids) is built on top of [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Scripts:setup_subject setup_subject_2]. The major goal is to apply BIDs format on the data structure. Besides of using BIDs structure, it added other useful features as well.

Setup_subject_3 has all the functions which exist in setup_subject_2 and works the same way with the same options as setup_subject_2.

===Recent updates===

* Change participant.tsv to participants.tsv

* Change default of mprage to be skipped

* Add TaskName field to Json files of functional data

* Add default dataset_description.json file and --datadesc option

* Add --dcm2niix option

* Add --intendedfor flag for adding "intendedfor" field to FieldMap

===Basic Usage===
setup_subject_3 [option] basedir subjectID

basedir is where you want the processed data to be stored in your Hoffman account,

subjectID is the subject folder name under /Dicom/data/YOURGROUP/ in Dicom server

<pre style="color: red">Use "setup_subject_bids_xa30" for data after Scanner upgrade to xa30 protocol </pre>

===Options:===

====Options for both BIDs mode and non-BIDs mode====
--download hostname,userid,path
download data from Dicom server to you hoffman account
It requires 3 argument, separated by comma(,)
(If you have downloaded the data already, this option is not needed)

1. hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server).
2. userid: Your Dicom server user ID
3. path: path to the subject data in dicom server (/Dicom/data/YOURGROUP)

-d (or --do) : use this option to specify the processing you want to add
After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: submit the job in batch mode

(Using option diags requires mcflirt, bet and melodic to be processed first)

-s (or --skip)
this option to specify the processing you want to skip
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_3 script

--spm
Set SPM compatibility

====Options for BIDs mode only====
--bids
BIDs format: specify using BIDs structure to group result files. However this option often being used with --config option to choose configuration file.
Without configuration file, the name conversion might not be correct under BIDs format rule.

--config FILEPATH/FILENAME
Specifying the BIDs naming configuration file path and name. Users should generate this file based on their data and BIDSs formatting rule. Here's more about the [[BIDs configuration file]].

--sessdir ses-NN
Specify session directory name. When the subject has multiple sessions, by default the processed results will all go under sub-xxxx/[anat | func | dwi | fmap] without separation based on sessions. If you want to have all the NIfTi converted files to be located in one specific session directory, you can use this option and all files will go under sub-xxxx/ses-NN/[anat | func | dwi | fmap ] (NN represents session number, e.g. 02)

--notar
No compression of dicom/ folder. Normally raw dicom data will be compressed into dicom*.tar.gz at the end of NiFTI convert. With this option, it will not compress.
This option is good when you know you want to run the setup_subject_3 script again and want to save time on compression and decompression of the data.
You should run without this option on the last run so it will save the disk usage.

--setgrp ''GROUPNAME''
Force the data's group to be set as the GROUPNAME specified. The GROUPNAME need to be an existing valid group name in Hoffman.

--pipeline ''PIPELINE_NAME''
Specify pipeline name used for analysis ( fsl is the default value)

--dcm2niix ''DCM2NIIX_VERSION''
Specify DCM2NIIX module version. The version has to match the available mricron module version in Hoffman2.
For example, to use mricron/20200331,
--dcm2niix 20200331
To find the version list to choose from, use
module av mricron

--datadesc /path/to/your/dataset_description.json
Specify dataset_description.json file location.
If there's no dataset_description.json file in your base bids directory and this option is not used, it will copy a default simple template to the bids folder. If your base directory has dataset_description.json already, it won't be over written.
This option should have the full path to your dataset_description followed.

--intendedfor
Add "intendedfor" field to fieldmap's json file with paths to the functional data.
This option is a flag and optional for Bids format.

When this flag is on, the script will look for files under dwi/ and func/ folder and add the file paths to *_epi.json files in fmap/ folder for "intendedfor" field.

===Data Structure===

=====Non-BIDs mode=====
folder subjectID will be created under basedir the user specified.
Then Dicom Raw data will be under dicom/ folder during NiFTI convert then compressed into dicom.tar.gz
Result of NiFTI convert will be under raw/ folder

ls basedir/subjectID
analysis behav dicom notes raw

=====BIDs mode=====
basedir/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/
|_
sourcedata/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
dicom/ setup_log.xxxxxxx
|_
derivatives/
|_
PipelineName/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/

===Examples: ===

Load the script module first:
module load ccnscripts

====NON-BIDs Mode====

Download data and run NIFTI convert
setup_subject_3 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ -s mprage basedir subjectID
( /dicom/data/YOURGROUP/subjectID is the path to the raw data in Dicom server. We skip mprage here since it will be run by default)

Download data and run NIFTI convert and other FSL processing:
setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download
setup_subject_3 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject_3 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject_3 -d mprage basedir subjectID

Skip mcflirt,bet,melodic,diags
setup_subject_3 -s mcflirt,bet,melodic,diags basedir subjectID

====BIDs mode====

Download data and run debabel with Bids format, skip mprage.

setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ --bids --config ~/bidsname-sub123.conf -s mprage basedir subjectID

===Notes===
Log File: provides useful details about what commands were run, their output and the script's status. It's located at the following location for bids mode and non-bids mode

BIDs mode

basedir/sourcedata/sub-subjectID/setup_log.date_numbers

Non-BIDs mode

basedir/subjectID/notes/setup_log.date_numbers

Hoffman2:Scripts:setup subject 3

2025-07-02T16:57:46Z

Hwang: /* Basic Usage */

==Setup Environment==
To use this script, load the ccnscripts module first:

module load ccnscripts

==Setup_subject script usage==
Setup_subject_3 (also named as setup_subject_bids) is built on top of [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Scripts:setup_subject setup_subject_2]. The major goal is to apply BIDs format on the data structure. Besides of using BIDs structure, it added other useful features as well.

Setup_subject_3 has all the functions which exist in setup_subject_2 and works the same way with the same options as setup_subject_2.

===Recent updates===

* Change participant.tsv to participants.tsv

* Change default of mprage to be skipped

* Add TaskName field to Json files of functional data

* Add default dataset_description.json file and --datadesc option

* Add --dcm2niix option

* Add --intendedfor flag for adding "intendedfor" field to FieldMap

===Basic Usage===
setup_subject_3 [option] basedir subjectID

basedir is where you want the processed data to be stored in your Hoffman account,

subjectID is the subject folder name under /Dicom/data/YOURGROUP/ in Dicom server

<pre style="color: red">Use "setup_subject_bids_xa30"
For data after Scanner upgrade to xa30 protocol </pre>

===Options:===

====Options for both BIDs mode and non-BIDs mode====
--download hostname,userid,path
download data from Dicom server to you hoffman account
It requires 3 argument, separated by comma(,)
(If you have downloaded the data already, this option is not needed)

1. hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server).
2. userid: Your Dicom server user ID
3. path: path to the subject data in dicom server (/Dicom/data/YOURGROUP)

-d (or --do) : use this option to specify the processing you want to add
After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: submit the job in batch mode

(Using option diags requires mcflirt, bet and melodic to be processed first)

-s (or --skip)
this option to specify the processing you want to skip
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_3 script

--spm
Set SPM compatibility

====Options for BIDs mode only====
--bids
BIDs format: specify using BIDs structure to group result files. However this option often being used with --config option to choose configuration file.
Without configuration file, the name conversion might not be correct under BIDs format rule.

--config FILEPATH/FILENAME
Specifying the BIDs naming configuration file path and name. Users should generate this file based on their data and BIDSs formatting rule. Here's more about the [[BIDs configuration file]].

--sessdir ses-NN
Specify session directory name. When the subject has multiple sessions, by default the processed results will all go under sub-xxxx/[anat | func | dwi | fmap] without separation based on sessions. If you want to have all the NIfTi converted files to be located in one specific session directory, you can use this option and all files will go under sub-xxxx/ses-NN/[anat | func | dwi | fmap ] (NN represents session number, e.g. 02)

--notar
No compression of dicom/ folder. Normally raw dicom data will be compressed into dicom*.tar.gz at the end of NiFTI convert. With this option, it will not compress.
This option is good when you know you want to run the setup_subject_3 script again and want to save time on compression and decompression of the data.
You should run without this option on the last run so it will save the disk usage.

--setgrp ''GROUPNAME''
Force the data's group to be set as the GROUPNAME specified. The GROUPNAME need to be an existing valid group name in Hoffman.

--pipeline ''PIPELINE_NAME''
Specify pipeline name used for analysis ( fsl is the default value)

--dcm2niix ''DCM2NIIX_VERSION''
Specify DCM2NIIX module version. The version has to match the available mricron module version in Hoffman2.
For example, to use mricron/20200331,
--dcm2niix 20200331
To find the version list to choose from, use
module av mricron

--datadesc /path/to/your/dataset_description.json
Specify dataset_description.json file location.
If there's no dataset_description.json file in your base bids directory and this option is not used, it will copy a default simple template to the bids folder. If your base directory has dataset_description.json already, it won't be over written.
This option should have the full path to your dataset_description followed.

--intendedfor
Add "intendedfor" field to fieldmap's json file with paths to the functional data.
This option is a flag and optional for Bids format.

When this flag is on, the script will look for files under dwi/ and func/ folder and add the file paths to *_epi.json files in fmap/ folder for "intendedfor" field.

===Data Structure===

=====Non-BIDs mode=====
folder subjectID will be created under basedir the user specified.
Then Dicom Raw data will be under dicom/ folder during NiFTI convert then compressed into dicom.tar.gz
Result of NiFTI convert will be under raw/ folder

ls basedir/subjectID
analysis behav dicom notes raw

=====BIDs mode=====
basedir/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/
|_
sourcedata/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
dicom/ setup_log.xxxxxxx
|_
derivatives/
|_
PipelineName/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/

===Examples: ===

Load the script module first:
module load ccnscripts

====NON-BIDs Mode====

Download data and run NIFTI convert
setup_subject_3 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ -s mprage basedir subjectID
( /dicom/data/YOURGROUP/subjectID is the path to the raw data in Dicom server. We skip mprage here since it will be run by default)

Download data and run NIFTI convert and other FSL processing:
setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download
setup_subject_3 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject_3 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject_3 -d mprage basedir subjectID

Skip mcflirt,bet,melodic,diags
setup_subject_3 -s mcflirt,bet,melodic,diags basedir subjectID

====BIDs mode====

Download data and run debabel with Bids format, skip mprage.

setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ --bids --config ~/bidsname-sub123.conf -s mprage basedir subjectID

===Notes===
Log File: provides useful details about what commands were run, their output and the script's status. It's located at the following location for bids mode and non-bids mode

BIDs mode

basedir/sourcedata/sub-subjectID/setup_log.date_numbers

Non-BIDs mode

basedir/subjectID/notes/setup_log.date_numbers

Hoffman2:Scripts:setup subject 3

2025-07-02T16:57:27Z

Hwang: /* Basic Usage */

==Setup Environment==
To use this script, load the ccnscripts module first:

module load ccnscripts

==Setup_subject script usage==
Setup_subject_3 (also named as setup_subject_bids) is built on top of [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Scripts:setup_subject setup_subject_2]. The major goal is to apply BIDs format on the data structure. Besides of using BIDs structure, it added other useful features as well.

Setup_subject_3 has all the functions which exist in setup_subject_2 and works the same way with the same options as setup_subject_2.

===Recent updates===

* Change participant.tsv to participants.tsv

* Change default of mprage to be skipped

* Add TaskName field to Json files of functional data

* Add default dataset_description.json file and --datadesc option

* Add --dcm2niix option

* Add --intendedfor flag for adding "intendedfor" field to FieldMap

===Basic Usage===
setup_subject_3 [option] basedir subjectID

basedir is where you want the processed data to be stored in your Hoffman account,

subjectID is the subject folder name under /Dicom/data/YOURGROUP/ in Dicom server

<pre style="color: red">Use "setup_subject_bids_xa30"<br>
For data after Scanner upgrade to xa30 protocol </pre>

===Options:===

====Options for both BIDs mode and non-BIDs mode====
--download hostname,userid,path
download data from Dicom server to you hoffman account
It requires 3 argument, separated by comma(,)
(If you have downloaded the data already, this option is not needed)

1. hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server).
2. userid: Your Dicom server user ID
3. path: path to the subject data in dicom server (/Dicom/data/YOURGROUP)

-d (or --do) : use this option to specify the processing you want to add
After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: submit the job in batch mode

(Using option diags requires mcflirt, bet and melodic to be processed first)

-s (or --skip)
this option to specify the processing you want to skip
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_3 script

--spm
Set SPM compatibility

====Options for BIDs mode only====
--bids
BIDs format: specify using BIDs structure to group result files. However this option often being used with --config option to choose configuration file.
Without configuration file, the name conversion might not be correct under BIDs format rule.

--config FILEPATH/FILENAME
Specifying the BIDs naming configuration file path and name. Users should generate this file based on their data and BIDSs formatting rule. Here's more about the [[BIDs configuration file]].

--sessdir ses-NN
Specify session directory name. When the subject has multiple sessions, by default the processed results will all go under sub-xxxx/[anat | func | dwi | fmap] without separation based on sessions. If you want to have all the NIfTi converted files to be located in one specific session directory, you can use this option and all files will go under sub-xxxx/ses-NN/[anat | func | dwi | fmap ] (NN represents session number, e.g. 02)

--notar
No compression of dicom/ folder. Normally raw dicom data will be compressed into dicom*.tar.gz at the end of NiFTI convert. With this option, it will not compress.
This option is good when you know you want to run the setup_subject_3 script again and want to save time on compression and decompression of the data.
You should run without this option on the last run so it will save the disk usage.

--setgrp ''GROUPNAME''
Force the data's group to be set as the GROUPNAME specified. The GROUPNAME need to be an existing valid group name in Hoffman.

--pipeline ''PIPELINE_NAME''
Specify pipeline name used for analysis ( fsl is the default value)

--dcm2niix ''DCM2NIIX_VERSION''
Specify DCM2NIIX module version. The version has to match the available mricron module version in Hoffman2.
For example, to use mricron/20200331,
--dcm2niix 20200331
To find the version list to choose from, use
module av mricron

--datadesc /path/to/your/dataset_description.json
Specify dataset_description.json file location.
If there's no dataset_description.json file in your base bids directory and this option is not used, it will copy a default simple template to the bids folder. If your base directory has dataset_description.json already, it won't be over written.
This option should have the full path to your dataset_description followed.

--intendedfor
Add "intendedfor" field to fieldmap's json file with paths to the functional data.
This option is a flag and optional for Bids format.

When this flag is on, the script will look for files under dwi/ and func/ folder and add the file paths to *_epi.json files in fmap/ folder for "intendedfor" field.

===Data Structure===

=====Non-BIDs mode=====
folder subjectID will be created under basedir the user specified.
Then Dicom Raw data will be under dicom/ folder during NiFTI convert then compressed into dicom.tar.gz
Result of NiFTI convert will be under raw/ folder

ls basedir/subjectID
analysis behav dicom notes raw

=====BIDs mode=====
basedir/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/
|_
sourcedata/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
dicom/ setup_log.xxxxxxx
|_
derivatives/
|_
PipelineName/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/

===Examples: ===

Load the script module first:
module load ccnscripts

====NON-BIDs Mode====

Download data and run NIFTI convert
setup_subject_3 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ -s mprage basedir subjectID
( /dicom/data/YOURGROUP/subjectID is the path to the raw data in Dicom server. We skip mprage here since it will be run by default)

Download data and run NIFTI convert and other FSL processing:
setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download
setup_subject_3 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject_3 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject_3 -d mprage basedir subjectID

Skip mcflirt,bet,melodic,diags
setup_subject_3 -s mcflirt,bet,melodic,diags basedir subjectID

====BIDs mode====

Download data and run debabel with Bids format, skip mprage.

setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ --bids --config ~/bidsname-sub123.conf -s mprage basedir subjectID

===Notes===
Log File: provides useful details about what commands were run, their output and the script's status. It's located at the following location for bids mode and non-bids mode

BIDs mode

basedir/sourcedata/sub-subjectID/setup_log.date_numbers

Non-BIDs mode

basedir/subjectID/notes/setup_log.date_numbers

Hoffman2:Scripts:setup subject 3

2025-07-02T16:55:42Z

Hwang: /* Basic Usage */

==Setup Environment==
To use this script, load the ccnscripts module first:

module load ccnscripts

==Setup_subject script usage==
Setup_subject_3 (also named as setup_subject_bids) is built on top of [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Scripts:setup_subject setup_subject_2]. The major goal is to apply BIDs format on the data structure. Besides of using BIDs structure, it added other useful features as well.

Setup_subject_3 has all the functions which exist in setup_subject_2 and works the same way with the same options as setup_subject_2.

===Recent updates===

* Change participant.tsv to participants.tsv

* Change default of mprage to be skipped

* Add TaskName field to Json files of functional data

* Add default dataset_description.json file and --datadesc option

* Add --dcm2niix option

* Add --intendedfor flag for adding "intendedfor" field to FieldMap

===Basic Usage===
setup_subject_3 [option] basedir subjectID

basedir is where you want the processed data to be stored in your Hoffman account,

subjectID is the subject folder name under /Dicom/data/YOURGROUP/ in Dicom server

*setup_subject_bids_xa30 [option] basedir subjectID<br>
For data after Scanner upgrade to xa30 protocol

===Options:===

====Options for both BIDs mode and non-BIDs mode====
--download hostname,userid,path
download data from Dicom server to you hoffman account
It requires 3 argument, separated by comma(,)
(If you have downloaded the data already, this option is not needed)

1. hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server).
2. userid: Your Dicom server user ID
3. path: path to the subject data in dicom server (/Dicom/data/YOURGROUP)

-d (or --do) : use this option to specify the processing you want to add
After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: submit the job in batch mode

(Using option diags requires mcflirt, bet and melodic to be processed first)

-s (or --skip)
this option to specify the processing you want to skip
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_3 script

--spm
Set SPM compatibility

====Options for BIDs mode only====
--bids
BIDs format: specify using BIDs structure to group result files. However this option often being used with --config option to choose configuration file.
Without configuration file, the name conversion might not be correct under BIDs format rule.

--config FILEPATH/FILENAME
Specifying the BIDs naming configuration file path and name. Users should generate this file based on their data and BIDSs formatting rule. Here's more about the [[BIDs configuration file]].

--sessdir ses-NN
Specify session directory name. When the subject has multiple sessions, by default the processed results will all go under sub-xxxx/[anat | func | dwi | fmap] without separation based on sessions. If you want to have all the NIfTi converted files to be located in one specific session directory, you can use this option and all files will go under sub-xxxx/ses-NN/[anat | func | dwi | fmap ] (NN represents session number, e.g. 02)

--notar
No compression of dicom/ folder. Normally raw dicom data will be compressed into dicom*.tar.gz at the end of NiFTI convert. With this option, it will not compress.
This option is good when you know you want to run the setup_subject_3 script again and want to save time on compression and decompression of the data.
You should run without this option on the last run so it will save the disk usage.

--setgrp ''GROUPNAME''
Force the data's group to be set as the GROUPNAME specified. The GROUPNAME need to be an existing valid group name in Hoffman.

--pipeline ''PIPELINE_NAME''
Specify pipeline name used for analysis ( fsl is the default value)

--dcm2niix ''DCM2NIIX_VERSION''
Specify DCM2NIIX module version. The version has to match the available mricron module version in Hoffman2.
For example, to use mricron/20200331,
--dcm2niix 20200331
To find the version list to choose from, use
module av mricron

--datadesc /path/to/your/dataset_description.json
Specify dataset_description.json file location.
If there's no dataset_description.json file in your base bids directory and this option is not used, it will copy a default simple template to the bids folder. If your base directory has dataset_description.json already, it won't be over written.
This option should have the full path to your dataset_description followed.

--intendedfor
Add "intendedfor" field to fieldmap's json file with paths to the functional data.
This option is a flag and optional for Bids format.

When this flag is on, the script will look for files under dwi/ and func/ folder and add the file paths to *_epi.json files in fmap/ folder for "intendedfor" field.

===Data Structure===

=====Non-BIDs mode=====
folder subjectID will be created under basedir the user specified.
Then Dicom Raw data will be under dicom/ folder during NiFTI convert then compressed into dicom.tar.gz
Result of NiFTI convert will be under raw/ folder

ls basedir/subjectID
analysis behav dicom notes raw

=====BIDs mode=====
basedir/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/
|_
sourcedata/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
dicom/ setup_log.xxxxxxx
|_
derivatives/
|_
PipelineName/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/

===Examples: ===

Load the script module first:
module load ccnscripts

====NON-BIDs Mode====

Download data and run NIFTI convert
setup_subject_3 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ -s mprage basedir subjectID
( /dicom/data/YOURGROUP/subjectID is the path to the raw data in Dicom server. We skip mprage here since it will be run by default)

Download data and run NIFTI convert and other FSL processing:
setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download
setup_subject_3 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject_3 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject_3 -d mprage basedir subjectID

Skip mcflirt,bet,melodic,diags
setup_subject_3 -s mcflirt,bet,melodic,diags basedir subjectID

====BIDs mode====

Download data and run debabel with Bids format, skip mprage.

setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ --bids --config ~/bidsname-sub123.conf -s mprage basedir subjectID

===Notes===
Log File: provides useful details about what commands were run, their output and the script's status. It's located at the following location for bids mode and non-bids mode

BIDs mode

basedir/sourcedata/sub-subjectID/setup_log.date_numbers

Non-BIDs mode

basedir/subjectID/notes/setup_log.date_numbers

Hoffman2:Scripts:setup subject 3

2025-07-02T16:55:18Z

Hwang: /* Basic Usage */

==Setup Environment==
To use this script, load the ccnscripts module first:

module load ccnscripts

==Setup_subject script usage==
Setup_subject_3 (also named as setup_subject_bids) is built on top of [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Scripts:setup_subject setup_subject_2]. The major goal is to apply BIDs format on the data structure. Besides of using BIDs structure, it added other useful features as well.

Setup_subject_3 has all the functions which exist in setup_subject_2 and works the same way with the same options as setup_subject_2.

===Recent updates===

* Change participant.tsv to participants.tsv

* Change default of mprage to be skipped

* Add TaskName field to Json files of functional data

* Add default dataset_description.json file and --datadesc option

* Add --dcm2niix option

* Add --intendedfor flag for adding "intendedfor" field to FieldMap

===Basic Usage===
setup_subject_3 [option] basedir subjectID

basedir is where you want the processed data to be stored in your Hoffman account,

subjectID is the subject folder name under /Dicom/data/YOURGROUP/ in Dicom server

* setup_subject_bids_xa30 [option] basedir subjectID<br>
For data after Scanner upgrade to xa30 protocol

===Options:===

====Options for both BIDs mode and non-BIDs mode====
--download hostname,userid,path
download data from Dicom server to you hoffman account
It requires 3 argument, separated by comma(,)
(If you have downloaded the data already, this option is not needed)

1. hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server).
2. userid: Your Dicom server user ID
3. path: path to the subject data in dicom server (/Dicom/data/YOURGROUP)

-d (or --do) : use this option to specify the processing you want to add
After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: submit the job in batch mode

(Using option diags requires mcflirt, bet and melodic to be processed first)

-s (or --skip)
this option to specify the processing you want to skip
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_3 script

--spm
Set SPM compatibility

====Options for BIDs mode only====
--bids
BIDs format: specify using BIDs structure to group result files. However this option often being used with --config option to choose configuration file.
Without configuration file, the name conversion might not be correct under BIDs format rule.

--config FILEPATH/FILENAME
Specifying the BIDs naming configuration file path and name. Users should generate this file based on their data and BIDSs formatting rule. Here's more about the [[BIDs configuration file]].

--sessdir ses-NN
Specify session directory name. When the subject has multiple sessions, by default the processed results will all go under sub-xxxx/[anat | func | dwi | fmap] without separation based on sessions. If you want to have all the NIfTi converted files to be located in one specific session directory, you can use this option and all files will go under sub-xxxx/ses-NN/[anat | func | dwi | fmap ] (NN represents session number, e.g. 02)

--notar
No compression of dicom/ folder. Normally raw dicom data will be compressed into dicom*.tar.gz at the end of NiFTI convert. With this option, it will not compress.
This option is good when you know you want to run the setup_subject_3 script again and want to save time on compression and decompression of the data.
You should run without this option on the last run so it will save the disk usage.

--setgrp ''GROUPNAME''
Force the data's group to be set as the GROUPNAME specified. The GROUPNAME need to be an existing valid group name in Hoffman.

--pipeline ''PIPELINE_NAME''
Specify pipeline name used for analysis ( fsl is the default value)

--dcm2niix ''DCM2NIIX_VERSION''
Specify DCM2NIIX module version. The version has to match the available mricron module version in Hoffman2.
For example, to use mricron/20200331,
--dcm2niix 20200331
To find the version list to choose from, use
module av mricron

--datadesc /path/to/your/dataset_description.json
Specify dataset_description.json file location.
If there's no dataset_description.json file in your base bids directory and this option is not used, it will copy a default simple template to the bids folder. If your base directory has dataset_description.json already, it won't be over written.
This option should have the full path to your dataset_description followed.

--intendedfor
Add "intendedfor" field to fieldmap's json file with paths to the functional data.
This option is a flag and optional for Bids format.

When this flag is on, the script will look for files under dwi/ and func/ folder and add the file paths to *_epi.json files in fmap/ folder for "intendedfor" field.

===Data Structure===

=====Non-BIDs mode=====
folder subjectID will be created under basedir the user specified.
Then Dicom Raw data will be under dicom/ folder during NiFTI convert then compressed into dicom.tar.gz
Result of NiFTI convert will be under raw/ folder

ls basedir/subjectID
analysis behav dicom notes raw

=====BIDs mode=====
basedir/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/
|_
sourcedata/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
dicom/ setup_log.xxxxxxx
|_
derivatives/
|_
PipelineName/
|_
sub-[subjectID]/
|_
[ses-SESSIONID]/
|_
anat/ dwi/ fmap/ func/

===Examples: ===

Load the script module first:
module load ccnscripts

====NON-BIDs Mode====

Download data and run NIFTI convert
setup_subject_3 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ -s mprage basedir subjectID
( /dicom/data/YOURGROUP/subjectID is the path to the raw data in Dicom server. We skip mprage here since it will be run by default)

Download data and run NIFTI convert and other FSL processing:
setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download
setup_subject_3 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject_3 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject_3 -d mprage basedir subjectID

Skip mcflirt,bet,melodic,diags
setup_subject_3 -s mcflirt,bet,melodic,diags basedir subjectID

====BIDs mode====

Download data and run debabel with Bids format, skip mprage.

setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ --bids --config ~/bidsname-sub123.conf -s mprage basedir subjectID

===Notes===
Log File: provides useful details about what commands were run, their output and the script's status. It's located at the following location for bids mode and non-bids mode

BIDs mode

basedir/sourcedata/sub-subjectID/setup_log.date_numbers

Non-BIDs mode

basedir/subjectID/notes/setup_log.date_numbers

Hoffman2:Scripts:clean up.sh

2025-06-10T22:24:32Z

Hwang:

This script is used to clean up the following files.

1. feat folders (+.feat)
2. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
3. files end with .con .grp .Icon .mat
4. tsplot
5. core.[0-9]

Load the module first
module load ccnscripts

<nowiki>*</nowiki> If you just want to see what files will be deleted without really deleting them, add --dryrun, e.g.

clean_up.sh -f --dryrun /PATH/TO/FOLDER

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For .con .grp .Icon .mat

clean_up.sh -g /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

For core.[0-9]

clean_up.sh -c /PATH/TO/FOLDER

Log File:<br>
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"<br>

<nowiki>*</nowiki> What if I want to recover some of the deleted files?

This script will move selected files to your $SCRATCH folder. In case you want to recover files being removed by this script, you can look for them under your $SCRATCH/YYYYMMDD_mmssms/ folder.

Hoffman2:Scripts:clean up.sh

2025-06-10T22:22:14Z

Hwang:

This script is used to clean up the following files.

1. feat folders (+.feat)
2. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
3. files end with .con .grp .Icon .mat
4. tsplot
5. core.[0-9]

Load the module first
module load ccnscripts

<nowiki>*</nowiki> If you just want to see what files will be deleted without really deleting them, add --dryrun, e.g.

clean_up.sh -c --dryrun /PATH/TO/FOLDER

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For .con .grp .Icon .mat

clean_up.sh -g /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

For core.[0-9]

clean_up.sh -c /PATH/TO/FOLDER

Log File:<br>
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"<br>

<nowiki>*</nowiki> What if I want to recover some of the deleted files?

This script will move selected files to your $SCRATCH folder. In case you want to recover files being removed by this script, you can look for them under your $SCRATCH/YYYYMMDD_mmssms/ folder.

Hoffman2:Scripts:clean up.sh

2025-06-10T22:21:39Z

Hwang:

This script is used to clean up the following files.

1. feat folders (+.feat)
2. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
3. files end with .con .grp .Icon .mat
4. tsplot
5. core.[0-9]

Load the module first
module load ccnscripts

<nowiki>*</nowiki> If you just want to see what files will be deleted without really deleting them, add --dryrun, e.g.

clean_up.sh -c --dryrun /PATH/TO/FOLDER

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For .con .grp .Icon .mat

clean_up.sh -g /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

For core.[0-9]

clean_up.sh -c /PATH/TO/FOLDER

Log File:<br>
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"

<nowiki>*</nowiki> What if I want to recover some of the deleted files?

This script will move selected files to your $SCRATCH folder. In case you want to recover files being removed by this script, you can look for them under your $SCRATCH/YYYYMMDD_mmssms/ folder.

Hoffman2:Scripts:clean up.sh

2025-06-10T22:21:20Z

Hwang:

This script is used to clean up the following files.

1. feat folders (+.feat)
2. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
3. files end with .con .grp .Icon .mat
4. tsplot
5. core.[0-9]

Load the module first
module load ccnscripts

<nowiki>*</nowiki> If you just want to see what files will be deleted without really deleting them, add --dryrun, e.g.

clean_up.sh -c --dryrun /PATH/TO/FOLDER

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For .con .grp .Icon .mat

clean_up.sh -g /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

For core.[0-9]

clean_up.sh -c /PATH/TO/FOLDER

Log File:<br>
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"

<nowiki>*</nowiki> What if I want to recover some of the deleted files?

This script will move selected files to your $SCRATCH folder. In case you want to recover files being removed by this script, you can look for them under your $SCRATCH/YYYYMMDD_mmssms/ folder.

Hoffman2:Scripts:clean up.sh

2025-06-10T22:18:09Z

Hwang:

This script is used to clean up the following files.

1. feat folders (+.feat)
2. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
3. files end with .con .grp .Icon .mat
4. tsplot
5. core.[0-9]

Load the module first
module load ccnscripts

<nowiki>*</nowiki> If you just want to see what files will be deleted without really deleting them, add --dryrun, e.g.

clean_up.sh -c --dryrun /PATH/TO/FOLDER

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For .con .grp .Icon .mat

clean_up.sh -g /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

For core.[0-9]

clean_up.sh -c /PATH/TO/FOLDER

Log File:<br>
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"

<nowiki>*</nowiki> What if I want to recover some of the deleted files?

This script will moved selected files to $SCRATCH folder. In case you want to recover files being cleaned up by this script, you can look for them in your $SCRATCH/$DATE/TARGET/FOLDERS folder

Hoffman2:Scripts:clean up.sh

2025-06-10T22:17:17Z

Hwang:

This script is used to clean up the following files.

1. feat folders (+.feat)
2. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
3. files end with .con .grp .Icon .mat
4. tsplot
5. core.[0-9]

Load the module first
module load ccnscripts

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For .con .grp .Icon .mat

clean_up.sh -g /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

For core.[0-9]

clean_up.sh -c /PATH/TO/FOLDER

<nowiki>*</nowiki> If you want to see what files will be deleted without really deleting them, use --dryrun, e.g.

clean_up.sh -c --dryrun /PATH/TO/FOLDER

Log File:<br>
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"

<nowiki>*</nowiki> What if I want to recover some of the deleted files?

This script will moved selected files to $SCRATCH folder. In case you want to recover files being cleaned up by this script, you can look for them in your $SCRATCH/$DATE/TARGET/FOLDERS folder

Hoffman2:Scripts:clean up.sh

2025-06-10T22:15:01Z

Hwang:

This script is used to clean up the following files.

1. feat folders (+.feat)
2. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
3. files end with .con .grp .Icon .mat
4. tsplot
5. core.[0-9]

Load the module first
module load ccnscripts

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For .con .grp .Icon .mat

clean_up.sh -g /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

For core.[0-9]

clean_up.sh -c /PATH/TO/FOLDER

* If you want to see what files will be deleted without really deleting them, use --dryrun, e.g.

clean_up.sh -c --dryrun /PATH/TO/FOLDER

Log File:<br>
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"

* What if I want to recover some of the deleted files?

This script will moved selected files to $SCRATCH folder. In case you want to recover files being cleaned up by this script, you can look for them in your $SCRATCH/DATE/TARGET/FOLDERS folder

Hoffman2:Scripts:clean up.sh

2025-05-19T22:36:29Z

Hwang:

This script is used to clean up the following files.

1. tsplot
2. feat folders (+.feat)
3. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
4. files end with .con .grp .Icon .mat

Load the module first
module load ccnscripts

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

Log File:<br>
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"

This script will moved selected files to $SCRATCH folder. In case you want to recover files being cleaned up by this script, you can look for them in your $SCRATCH folder

Hoffman2:Scripts:clean up.sh

2025-05-19T22:35:59Z

Hwang:

This script is used to clean up the following files.

1. tsplot
2. feat folders (+.feat)
3. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
4. files end with .con .grp .Icon .mat

Load the module first
module load ccnscripts

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

Log File:
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"

This script will moved selected files to $SCRATCH folder. In case you want to recover files being cleaned up by this script, you can look for them in your $SCRATCH folder

Hoffman2:Scripts:clean up.sh

2025-05-19T22:35:33Z

Hwang:

This script is used to clean up the following files.

1. tsplot
2. feat folders (+.feat)
3. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
4. files end with .con .grp .Icon .mat

Load the module first
module load ccnscripts

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

Log File:
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"

This script will moved selected files to $SCRATCH folder. In case you want to recover files being cleaned up by this script, you can look for them in your $SCRATCH folder

Hoffman2:Scripts:clean up.sh

2025-05-19T22:35:16Z

Hwang:

This script is used to clean up the following files.

1. tsplot
2. feat folders (+.feat)
3. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
4. files end with .con .grp .Icon .mat

Load the module first
module load ccnscripts

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

Log File:
A log file will be generated under the folder where you run it, named as "clean_up_log.YYYYMMDD_ss"

This script will moved selected files to $SCRATCH folder. In case you want to recover files being cleaned up by this script, you can look for them in your $SCRATCH folder

Hoffman2:Scripts:clean up.sh

2025-05-19T22:26:16Z

Hwang:

This script is used to clean up the following files.

1. tsplot
2. feat folders (+.feat)
3. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
4. files end with .con .grp .Icon .mat

Load the module first
module load ccnscripts

For clean up feat folders,

clean_up.sh -f /PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o /PATH/TO/FOLDER

For tsplot

clean_up.sh -t /PATH/TO/FOLDER

This script will moved selected files to $SCRATCH folder. In case you want to recover files being cleaned up by this script, you can look for them in your $SCRATCH folder

Hoffman2:Scripts:clean up.sh

2025-05-19T22:20:51Z

Hwang: Created page with "This script is used to clean up certain FSL processing files. 1. tsplot 2. feat folders (+.feat) 3. FSL stdout and stderr files (such as *.e28678.8, *.o4436) 4. files end with .con .grp .Icon .mat Load the module first module load ccnscripts For clean up feat folders, clean_up.sh -f PATH/TO/FOLDER For .o and .e files clean_up.sh -o PATH/TO/FOLDER For tsplot clean_up.sh -t PATH/TO/FOLDER"

This script is used to clean up certain FSL processing files.

1. tsplot
2. feat folders (+.feat)
3. FSL stdout and stderr files (such as *.e28678.8, *.o4436)
4. files end with .con .grp .Icon .mat

Load the module first
module load ccnscripts

For clean up feat folders,

clean_up.sh -f PATH/TO/FOLDER

For .o and .e files

clean_up.sh -o PATH/TO/FOLDER

For tsplot

clean_up.sh -t PATH/TO/FOLDER

Hoffman2:Scripts

2025-05-19T22:15:01Z

Hwang:

[[Hoffman2|Back to all things Hoffman2]]

When you encounter a computer problem, it is best to find a systematic solution in the form of a script or program. This lets you be prepared to handle the problem the next time you encounter it because let's face it, history has a way of repeating itself.

Here-in lies a collection of the scripts we have built up in the Hoffman2 FMRI group for solving our most common problems. Each script's help output is provided for searching convenience as well as example usage cases for each script.

==clean_up.sh==
Clean up files such as tsplot and FSL stderr
:[[Hoffman2:Scripts:clean_up.sh|clean_up.sh]]

==clean_me.py==
How to clean up after yourself and maintain within your quota space.
:[[Hoffman2:Scripts:clean_me.py|clean_me.py]]

==clear_scratch.sh==
Clear out all the temporary files you kept in your [[Hoffman2:Introduction#Temporary_Storage|scratch]] directory.
:[[Hoffman2:Scripts:clear_scratch.sh|clear_scratch.sh]]





==fix_perms.sh==
Collaboration is one of the best ways to further science. So if your labmate can't work on the data you just processed for her, science has a hard time moving forward. Fix those permissions and collaborate!
:[[Hoffman2:Scripts:fix_perms.sh|fix_perms.sh]]

==getDicomDate.py==
All you want to know if when the DICOM got created and you don't have time to learn how to read DICOM files byte-wise. Just run this script.
:[[Hoffman2:Scripts:getDicomDate.py|getDicomDate.py]]



==matlab_license_check.sh==
MATLAB Licenses are as valuable as gold at times of heavy computing on Hoffman2. Use this script to find out if there is one with your name on it, or to find out who to go yell at for using too many licenses.
:[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]






==setup_subject==
Transfer Dicom data from the Dicom server and do NIFTI Convert and other processes.
:[[Hoffman2:Scripts:setup_subject|setup_subject]]
:[[Hoffman2:Scripts:setup_subject_3|setup_subject_3]]

==dcmheader.py==
Read, edit Dicom file header information
:[[Hoffman2:Scripts:dcmheader.py|dcmheader.py]]

==gen_movie.py==
Convert MRI file into a movie
:[[Hoffman2:Scripts:gen_movie.py|gen_movie.py]]

Hoffman2:Software Tools:Osprey

2025-03-13T18:17:59Z

Hwang: /* Osprey */

==Osprey==

1. Start an interactive session by, for example
qrsh -l h_rt=2:00:00,h_data=24G

2. In the work node, run the following commands

module load matlab/R2020a
export MATLABPATH=/u/project/CCN/apps/spm12
matlab

The command "matlab" will open Matlab GUI interface

3. Install "GUI Layout" and "Widgets" Toolboxes

1) Open Matlab GUI and go to “Home” -> “Open” and navigate to /u/project/CCN/apps/matlab, choose file

GUI Layout Toolbox 2.4.1.mltbx

2) Then click “Open” button on the bottom. This will install GUI Layout toolbox.

3) Repeat these steps for Widgets.Toolbox.1.5.1.mltbx.

4. Start Osprey<br>
Go back to Matlab prompt and type in

Osprey

Osprey GUI will start

Hoffman2:Software Tools:Osprey

2025-03-13T18:12:33Z

Hwang:

==Osprey==

1. Start an interactive session by, for example
qrsh -l h_rt=2:00:00,h_data=24G

2. In the work node, run the following commands

module load matlab/R2020a
export MATLABPATH=/u/project/CCN/apps/spm12
matlab

The command "matlab" will open Matlab GUI interface

3. Install "GUI Layout" and "Widgets" Toolboxes

1) Open Matlab GUI and go to “Home” -> “Open” and navigate to /u/project/CCN/apps/matlab, choose file

GUI Layout Toolbox 2.4.1.mltbx

2) Then click “Open” button on the bottom. This will install GUI Layout toolbox.

3) Repeat these steps for Widgets.Toolbox.1.5.1.mltbx.

4. Start Osprey
Go back to Matlab prompt and type in

Osprey

Osprey GUI will start

Hoffman2:Software Tools:Osprey

2025-03-13T18:08:59Z

Hwang: /* Osprey */

==Osprey==

1. Start an interactive session by, for example
qrsh -l h_rt=2:00:00,h_data=24G

2. In the work node, run the following commands

module load matlab/R2020a
export MATLABPATH=/u/project/CCN/apps/spm12
matlab

The command "matlab" will open Matlab GUI interface

3. Install "GUI Layout" and "Widgets" Toolboxes

Open Matlab GUI and go to “Home” -> “Open”
Then navigate to /u/project/CCN/apps/matlab and choose file

GUI Layout Toolbox 2.4.1.mltbx

Then click “Open” button on the bottom.
This will install GUI Layout toolbox.

Repeat these steps for Widgets.Toolbox.1.5.1.mltbx.

4. Start Osprey
Go back to Matlab prompt and type in

Osprey

Osprey GUI will start

Hoffman2:Software Tools:Osprey

2025-03-13T18:07:16Z

Hwang:

==Osprey==

1. Start an interactive session by, for example
qrsh -l h_rt=2:00:00,h_data=24G

2. In the work node, run the following commands

module load matlab/R2020a
export MATLABPATH=/u/project/CCN/apps/spm12
matlab

The command "matlab" will open Matlab GUI interface

3. Install "GUI Layout" and "Widgets" Toolboxes

Open Matlab GUI and go to “Home” -> “Open”
Then navigate to /u/project/CCN/apps/matlab and then choose file

GUI Layout Toolbox 2.4.1.mltbx

Then click “Open” button on the bottom.
This will install GUI Layout toolbox.

Repeat these steps for Widgets.Toolbox.1.5.1.mltbx.
Then follow the same steps I sent yesterday to start Osprey and it should work.

Hoffman2:Software Tools:Osprey

2025-03-13T18:05:53Z

Hwang: Created page with "==Osprey== 1. Start an interactive session by, for example qrsh -l h_rt=2:00:00,h_data=24G 2. In the work node, run the following commands module load matlab/R2020a export MATLABPATH=/u/project/CCN/apps/spm12 matlab The command "matlab" will open Matlab GUI interface 3. Install Toolboxes"

Hoffman2:Software Tools

2025-03-13T18:01:35Z

Hwang:

[[Hoffman2|Back to all things Hoffman2]]

There is a CCN usergroup on Hoffman2 which is maintained for groups doing Neuroimaging work at UCLA. Tools like FSL, FreeSurfer, AFNI and Nibabel are maintained for this group separate from normal Hoffman2 programs. In order to take advantage of these tools, you need to load the modules into the interactive mode or listed in your batch mode scripts.

module load appname/version

Below is a list of the available software tools. We will do our best to update it as changes are made.

*Do not load matlab and freesurfer or matlab and RStudio as it will cause errors.

==AFNI==
[http://afni.nimh.nih.gov/afni/ Official Webste]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
|20.1.00 || || New
|- class="ccn-table-odd"
|19.0.15 || 2019.02.20 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
|17.2.07 || 2017.02.07 || Default
|- class="ccn-table-odd"
|16.3.1 || 2016.11.20 ||
|- class="ccn-table-even""
|2011.12.21.1014 ||2012.03.19 ||
|}

==ANTS==
[http://stnava.github.io/ANTs/ Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
|ants-2.3.1 || || New
|- class="ccn-table-odd"
|ants-2.2.0 || 2019.03.25 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
|ants-2.1.0-redhat || 2015.01.23 || Default
|}

==ASHS==
[https://www.nitrc.org/projects/ashs| Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 20180720 || 2018.07.20 || New
|- class="ccn-table-odd"
| 2017-02 || 2017.06.08 ||
|- class="ccn-table-odd" style="background-color:#ffffcc;"
| Rev-103 || 2016.02.24 || Default
|}

==BrainSuite==
[http://brainsuite.org/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 19a || 2019.02.19 || Default
|- class="ccn-table-odd"
| 18a || ||
|- class="ccn-table-even"
| 17a || ||
|- class="ccn-table-odd"
| 15c || 2016.02.18 || No longer supported
|}

==BrainAgeR==
[https://github.com/james-cole/brainageR Official Website]
[[Hoffman2:Software Tools:BrainAgeR|Load BrainAgeR module]]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 19a || 2019.02.19 || Default
|- class="ccn-table-odd"
| 18a || ||
|- class="ccn-table-even"
| 17a || ||
|- class="ccn-table-odd"
| 15c || 2016.02.18 || No longer supported
|}

==brms==
R library [http://https://mc-stan.org/users/interfaces/brms Official Website]

[[Hoffman2:Software Tools:brms|How to load]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 2.17.0 || 2022.06.10 || Default
|}



==Caret==
[http://brainvis.wustl.edu/wiki/index.php/Caret:About Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 5.65 (2012.01.27) || 2013.07.15 || Default, not folded into the main profile
|}

==ccn_py37==
Conda virtual environment with nibabel, nilearn, pydicom, pandas, scikit-learn, scipy

[[Hoffman2:Software Tools:ccn_py37|How to load]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| 1.0 || 2021.05.24 || CentOS 7 with Conda
|}

==Chronux==
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 2.10 || 2013.02.26 || Current
|}

==CONN==
[https://web.conn-toolbox.org/ Official Website]

[[Hoffman2:Software Tools:CONN|Load CONN module]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 19.b || || New
|- class="ccn-table-odd"
| 18.b || ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 17.f || || Default
|}

==dcm2nii==
[http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 2013.06.06 || 2014.03.06 ||
|- class="ccn-table-even"
| 2011.11.11 || circa 2011 || Current
|}

==dmctk==
[https://dicom.offis.de/dcmtk.php.en Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 3.6.0 || 2017.05.17 || Current
|- class="ccn-table-even"
| 3.6.6 || 2021.02.16
|}

==DTIprep==
[https://www.nitrc.org/projects/dtiprep/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.2.4 || 2017.12.21 ||
|- class="ccn-table-even"
| 1.2.9 || 2018.03.20 || Current
|}

==DSI Studio==
[https://dsi-studio.labsolver.org/ Official Website]

===Please note DSI studio only works with NoMachine===

[[Hoffman2:Software Tools:DSI Studio|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| "Chen" Release || 2023.07.06 || Current
|}

==dmriprep==
[https://github.com/nipreps/dmriprep Official Website]

[[Hoffman2:Software Tools:dmriprep|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.4.0 || 2020.12.10 || Current
|}

==EEGLAB==
[http://sccn.ucsd.edu/eeglab/ Official Website]

[http://sccn.ucsd.edu/wiki/EEGLAB_revision_history Release Notes]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 13.1.1b || 2014.01.29 ||
|- class="ccn-table-even"
| 12.0.2.5b || 2013.11.14 ||
|- class="ccn-table-odd"
| 11.0.5.4b || 2013.11.14 ||
|- class="ccn-table-even"
| 12.0.0.0b || 2012.12.10 ||
|- class="ccn-table-odd"
| 11.0.0.0b || 2012.02.21 ||
|- class="ccn-table-even"
| 10.2.5.8b || 2012.02.21 ||
|}

==ENIGMA==
[https://www.nitrc.org/projects/dtiprep/ Official Website]

[[Hoffman2:Software Tools:Enigma|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 20210422 || 2021.04.22 || Current
|}

==ENIGMA HALFpipe==
[https://github.com/HALFpipe/HALFpipe Official Website]

[[Hoffman2:Software Tools:HALfpipe|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.1.1 || 2021.08.27 || Current
|}

==FastSurfer==
[https://github.com/Deep-MI/FastSurfer/ Official Website]

[[Hoffman2:Software Tools:FastSurfer|Usage]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 202102 || 2021.03.01 || Current
|}

==FIT==
[https://trendscenter.org/software/fit/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| FITv2.0d || 2021.01.13 ||
|- class="ccn-table-even"
| FITv2.0e || 2021.01.13 ||
|}

==FIX==
[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide Official Website]

[[Hoffman2:Software Tools:Fix|Use Fix in Hoffman]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.06.15 || 2021.12.01 ||
|}

==FMRIprep==
[https://fmriprep.readthedocs.io/en/stable/usage.html Official Website]

[[Hoffman2:Software Tools:FMRIprep|Load pre-requisite modules]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 23.1.3 ||2023.08.22 || Use Apptainer module
|- class="ccn-table-odd"
| 20.2.1 ||2021.05.13 || In Singularity
|- class="ccn-table-even"
| 20.2.0rc0 || ||
|- class="ccn-table-odd"
| 20.1.1 || || * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-even"
| 1.4.0 || 2019.01.11 || Default * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-odd"
| 1.3.2 || 2019.01.11 || * [[#Known_issue_2 |known Issue ]]
|}

<div id="Known_issue_2" style="display:inline;">Known issues: please see [https://github.com/nipreps/fmriprep/blob/master/.versions.json version history] </div>

==FreeSurfer==
[http://surfer.nmr.mgh.harvard.edu/ Official Website]

[http://freesurfer.net/fswiki/ReleaseNotes Release Notes]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 7.2.0 || 2021.11.29 ||
|- class="ccn-table-odd"
| 7.1.1 || 2021.02.26 ||
|- class="ccn-table-even"
| 6.0.0 || 2017.01.18 || CentOS 6 only
|}



==FSL==
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]

[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Revision History]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 6.0.4 || 2021.01.25|| new
|- class="ccn-table-odd"
| 6.0.3 || 2021.09.30||
|- class="ccn-table-even"
| 6.0.1 || 2019.03.01 ||
|- class="ccn-table-odd"
| 6.0.0 || 2018.10.23 ||
|- class="ccn-table-even"
| 5.0.11 || 2018.03.19 ||
|- class="ccn-table-odd"
| 5.0.10 || 2017.04.24 || * [[#Known_issue_1 |Known Issue ]]
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 5.0.9 || 2015.10.02 || Default
|- class="ccn-table-odd"
| 5.0.8 || 2014.12.03 ||
|- class="ccn-table-even"
| 5.0.7 || 2013.10.17 ||
|- class="ccn-table-odd"
| 5.0.6 || 2013.12.18 || (2013.12.18-2014.10.10)
|- class="ccn-table-odd"
| 4.1.9 || 2011.12.01 ||
|- class="ccn-table-even"
| 4.0.4 || circa 2008 ||
|}

<div id="Known_issue_1" style="display:inline;">Known issue: 5.0.10 fsleyes crash on x2go</div>

==FSL_MRS==
[https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/index.html# Official Website]

[https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/changelog.html Revision History]

[[Hoffman2:Software Tools:FSL_MRS|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 2.1.12 || 2023.08.22|| new

|}

==ggseg==
[https://github.com/ggseg/ggseg Official Website]

[[Hoffman2:Software Tools:ggseg|Load pre-requisite modules]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| v1.6.5.9000 || 2023.03.1 ||
|- class="ccn-table-even"
|}

* Note: ggsegExtra and ggseg3d are also available under these libraries

==gift==
[https://trendscenter.org/software/gift/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| GroupICATv4.0b || 2017.11.14 ||
|- class="ccn-table-even"
| GroupICATv4.0c || 2021.01.04 ||
|}

==gradunwarp==
[https://github.com/Washington-University/gradunwarp Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.1.0 || 2019.06.04 ||
|}

==HCP Benchwork ==
[https://www.humanconnectome.org/software/connectome-workbench Official Website]
* Note: module name: hcp
[[Hoffman2:Software Tools:HCPBench|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 1.3.2 || 2019.05.22 || New
|- class="ccn-table-odd"
| 1.2.3 || 2018.02.13 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 1.1.1 || 2016.02.18 || Default
|- class="ccn-table-odd"
| 1.0 || ||
|- class="ccn-table-even"
| 0.84 || ||
|}

==ICA-AROMA==

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 0.4.5 || || New
|- class="ccn-table-odd" style="background-color:#ffffcc;"
| 0.4.1-beta || || Default
|}

* Note: Python 2.7 available for v0.4.5, module name: ica-aroma_py27.
[[Hoffman2:Software Tools:ica-aroma_py27|Load ica-aroma_py27 module]]

==ITKGray==
[http://vistalab.stanford.edu/newlm/index.php/ItkGray Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 080803 || 2009.11.19 || Default
|- class="ccn-table-even"
| 080128 || 2009.11.13 ||
|}

==ITKSnap==
[http://www.itksnap.org/pmwiki/pmwiki.php Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 3.4.0.QT4 || 2016.02.24 || Default
|- class="ccn-table-even"
| 3.6.0.QT4 || 2021.03.02 ||
|- class="ccn-table-odd"
| 3.8.0.QT4 || 2021.03.02 || Default
|}

==kwave==
[http://www.k-wave.org/doxygen/index.html Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 1.3 || 2020.07.20 || Current
|}

==MANGO==

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 20190905 || || Current
|}

==MRIQC==
[https://mriqc.readthedocs.io/en/latest/ Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.16.1 || 2021.03.08 || Current
|}

==NDATools==
[https://github.com/NDAR/nda-tools Official Website]

[[Hoffman2:Software Tools:NDATools|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.2.3 || 2021.03.04 || Current
|}

==OpenSmile==
[https://www.audeering.com/opensmile/ Official Website]

[[Hoffman2:Software Tools:OpenSmile|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 3.0.0 || 2021.03.23 || Current
|}

==Osprey==
[https://schorschinho.github.io/osprey/]
[[Hoffman2:Software Tools:Osprey|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 2.9.6 || 2025.03.13 || Current
|}

==Profumo==
[https://git.fmrib.ox.ac.uk/samh/profumo Official Website]

[[Hoffman2:Software Tools:Profumo|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.11.3 || 2021.06.22 || Current
|}



==RATS==
[https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 060419 || 2019.06.04 || Current
|}

==RStan==
[https://mc-stan.org/ Official Website]

[[Hoffman2:Software Tools:Rstan|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 4.1.2 || 2022.04.11 || Current
|}

==SPM==
[http://www.fil.ion.ucl.ac.uk/spm/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Last Patch Applied
! class="ccn-table-header"| Last Checked Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| SPM12-standalone || || || Current
|- class="ccn-table-even"
| SPM12 || || ||
|- class="ccn-table-odd"
| SPM8 || 5236 || 2014.01 ||
|- class="ccn-table-even"
| SPM5 || Unknown || N/A || No longer supported
|}

==TrackVis/Diffusion Toolkit==
[http://trackvis.org/ Official Website 1]

[http://trackvis.org/dtk/ Official Website 2]
{| class="wikitable"
! class="ccn-table-header"| Tool
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Last Checked Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| TrackVis || 0.5.2.2 || 2014.03.06 ||
|- class="ccn-table-even"
| Diffusion Toolkit || 0.6.2.2 || 204.03.06 ||
|}

==WEKA==
[http://www.cs.waikato.ac.nz/ml/weka/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| 3.8.1 || ||
|- class="ccn-table-odd"
| 3.7.10 || 2014.03.03 ||
|- class="ccn-table-even"
| 3.6.5 || circa 2011.08 ||
|}



==External Links==
*[https://www.hoffman2.idre.ucla.edu/software/ Other Hoffman2 Software]

Incidental Finding Report Tool

2024-11-15T19:01:47Z

Hwang:

== Incidental Finding Report Tool ==

[[File:Incidental finding report flow.png|700px]]

1. Create a folder and put in all your images and movie files you want to send to the radiologist. <span style="color:#ff0000">'''Please circle the area where you consider an anomaly'''</span>.

* The images should include '''T1''' and '''T2''', and are saved in png or jpeg/jpg formats.

* (Optional) You can create a movie from MRI images using CCN script: [[Hoffman2:Scripts:gen_movie.py|gen_movie.py]]

* Name your folder contains all the files with your lab name and subject ID.

2. Compress the folder with zip, and make sure it's named with your lab name+subject ID.

* The compressed file should end with ".zip"

3. Upload the zip file to the Box folder, “CCN_report/YOURGROUP”, which should be shared with your lab.

* <span style="color:#ff0000">'''Before you upload the files, please make sure the images and videos are in good quality so the radiologist can make the correct decision based on it.'''</span>

If your lab does not have a Box group folder shared by us, please contact the following so we can set one up for you.

ccnsupport@g.ucla.edu

What will happen after you upload the zip file:

Our script will check the Box folder once a day and if there’s a new zip file, it will unzip it and then send an email to the radiologist with the images attached.

It will also send the link of the movie file.

Incidental Finding Report Tool

2024-11-15T19:00:54Z

Hwang:

== Incidental Finding Report Tool ==

[[File:Incidental finding report flow.png|700px]]

1. Create a folder and put in all your images and movie files you want to send to the radiologist. <span style="color:#ff0000">'''Please circle the area where you consider an anomaly'''</span>.

* The images should include '''T1''' and '''T2''', and are in png or jpeg/jpg formats.

* (Optional) You can create a movie from MRI images using CCN script: [[Hoffman2:Scripts:gen_movie.py|gen_movie.py]]

* Name your folder contains all the files with your lab name and subject ID.

2. Compress the folder with zip, and make sure it's named with your lab name+subject ID.

* The compressed file should end with ".zip"

3. Upload the zip file to the Box folder, “CCN_report/YOURGROUP”, which should be shared with your lab.

* <span style="color:#ff0000">'''Before you upload the files, please make sure the images and videos are in good quality so the radiologist can make the correct decision based on it.'''</span>

If your lab does not have a Box group folder shared by us, please contact the following so we can set one up for you.

ccnsupport@g.ucla.edu

What will happen after you upload the zip file:

Our script will check the Box folder once a day and if there’s a new zip file, it will unzip it and then send an email to the radiologist with the images attached.

It will also send the link of the movie file.