Hoffman2:Software Tools: Difference between revisions
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Below is a list of the available software tools. We will do our best to update it as changes are made. | 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== | ==AFNI== | ||
Line 73: | Line 74: | ||
|} | |} | ||
==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 | |||
|} | |||
<!-- | |||
==C3D== | ==C3D== | ||
--> | |||
==Caret== | ==Caret== | ||
Line 85: | Line 116: | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5.65 (2012.01.27) || 2013.07.15 || Default, not folded into the main profile | | 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 | |||
|} | |} | ||
Line 113: | Line 158: | ||
| 17.f || || Default | | 17.f || || Default | ||
|} | |} | ||
==dcm2nii== | ==dcm2nii== | ||
Line 152: | Line 198: | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 1.2.9 || 2018.03.20 || Current | | 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 | |||
|} | |} | ||
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| 20210422 || 2021.04.22 || Current | | 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== | ==FastSurfer== | ||
[https://github.com/Deep-MI/FastSurfer/ Official Website] | [https://github.com/Deep-MI/FastSurfer/ Official Website] | ||
[[Hoffman2:Software Tools:FastSurfer|Usage]] | |||
{| class="wikitable" | {| class="wikitable" | ||
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|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| FITv2.0e || 2021.01.13 || | | 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 || | |||
|} | |} | ||
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[https://fmriprep.readthedocs.io/en/stable/usage.html Official Website] | [https://fmriprep.readthedocs.io/en/stable/usage.html Official Website] | ||
[[Hoffman2:Software Tools: FMRIprep|Load pre-requisite modules]] | [[Hoffman2:Software Tools:FMRIprep|Load pre-requisite modules]] | ||
{| class="wikitable" | {| class="wikitable" | ||
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! class="ccn-table-header"| Install Date | ! class="ccn-table-header"| Install Date | ||
! class="ccn-table-header"| Notes | ! class="ccn-table-header"| Notes | ||
|- class="ccn-table- | |- 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 | | 20.2.1 ||2021.05.13 || In Singularity | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
Line 247: | Line 353: | ||
! class="ccn-table-header" | Notes | ! class="ccn-table-header" | Notes | ||
|- class="ccn-table- | |- class="ccn-table-even" style="background-color:#E5FFCC;" | ||
| 7.1.1 || | | 7.2.0 || 2021.11.29 || | ||
|- class="ccn-table-odd" | |||
| 7.1.1 || 2021.02.26 || | |||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 6.0.0 || 2017.01.18 || | | 6.0.0 || 2017.01.18 || CentOS 6 only | ||
|} | |||
<!-- | |||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5.3.0-HCP || 2013.05.13 || | | 5.3.0-HCP || 2013.05.13 || | ||
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|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 4.0.5 || circa 2008 || | | 4.0.5 || circa 2008 || | ||
--> | |||
==FSL== | ==FSL== | ||
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|- class="ccn-table-even" style="background-color:#E5FFCC;" | |- class="ccn-table-even" style="background-color:#E5FFCC;" | ||
| 6.0.4 || || new | | 6.0.4 || 2021.01.25|| new | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 6.0.3 || || | | 6.0.3 || 2021.09.30|| | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 6.0.1 || 2019.03.01 || | | 6.0.1 || 2019.03.01 || | ||
Line 304: | Line 416: | ||
<div id="Known_issue_1" style="display:inline;">Known issue: 5.0.10 fsleyes crash on x2go</div> | <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== | ==gift== | ||
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| 1.1.0 || 2019.06.04 || | | 1.1.0 || 2019.06.04 || | ||
|} | |} | ||
Line 335: | Line 478: | ||
[https://www.humanconnectome.org/software/connectome-workbench Official Website] | [https://www.humanconnectome.org/software/connectome-workbench Official Website] | ||
* Note: module name: hcp | * Note: module name: hcp | ||
[[Hoffman2:Software Tools:HCPBench|Usage]] | |||
{| class="wikitable" | {| class="wikitable" | ||
! class="ccn-table-header" | Version | ! class="ccn-table-header" | Version | ||
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| 0.84 || || | | 0.84 || || | ||
|} | |} | ||
==ICA-AROMA== | ==ICA-AROMA== | ||
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* Note: Python 2.7 available for v0.4.5, module name: ica-aroma_py27. | * 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]] | [[Hoffman2:Software Tools:ica-aroma_py27|Load ica-aroma_py27 module]] | ||
==ITKGray== | ==ITKGray== | ||
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| 080128 || 2009.11.13 || | | 080128 || 2009.11.13 || | ||
|} | |} | ||
==ITKSnap== | ==ITKSnap== | ||
Line 405: | Line 550: | ||
| 1.3 || 2020.07.20 || Current | | 1.3 || 2020.07.20 || Current | ||
|} | |} | ||
==MANGO== | ==MANGO== | ||
Line 414: | Line 560: | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 20190905 || || Current | | 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 | |||
|} | |} | ||
Line 428: | Line 586: | ||
| 0.2.3 || 2021.03.04 || Current | | 0.2.3 || 2021.03.04 || Current | ||
|} | |} | ||
==OpenSmile== | ==OpenSmile== | ||
Line 440: | Line 599: | ||
| 3.0.0 || 2021.03.23 || Current | | 3.0.0 || 2021.03.23 || Current | ||
|} | |} | ||
==Profumo== | ==Profumo== | ||
Line 453: | Line 613: | ||
| 0.11.3 || 2021.06.22 || Current | | 0.11.3 || 2021.06.22 || Current | ||
|} | |} | ||
<!--==Pytorch== | |||
[[Hoffman2:Software Tools:Pytorch|Usage]] | |||
{| class="wikitable" | |||
! class="ccn-table-header"| Version Number | |||
! class="ccn-table-header"| Install Date | |||
! class="ccn-table-header"| Notes | |||
|- class="ccn-table-odd" style="background-color:#E5FFCC;" | |||
| 1.8.0 || 2021.04.20 || CentOS 7 and GPU | |||
|} | |||
--> | |||
==RATS== | ==RATS== | ||
[https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website] | [https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website] | ||
Line 464: | Line 636: | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 060419 || 2019.06.04 || Current | | 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 | |||
|} | |} | ||
Latest revision as of 16:59, 13 December 2023
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
Version | Install Date | Notes |
---|---|---|
20.1.00 | New | |
19.0.15 | 2019.02.20 | |
17.2.07 | 2017.02.07 | Default |
16.3.1 | 2016.11.20 | |
2011.12.21.1014 | 2012.03.19 |
ANTS
Version | Install Date | Notes |
---|---|---|
ants-2.3.1 | New | |
ants-2.2.0 | 2019.03.25 | |
ants-2.1.0-redhat | 2015.01.23 | Default |
ASHS
Version | Install Date | Notes |
---|---|---|
20180720 | 2018.07.20 | New |
2017-02 | 2017.06.08 | |
Rev-103 | 2016.02.24 | Default |
BrainSuite
Version | Install Date | Notes |
---|---|---|
19a | 2019.02.19 | Default |
18a | ||
17a | ||
15c | 2016.02.18 | No longer supported |
BrainAgeR
Official Website Load BrainAgeR module
Version | Install Date | Notes |
---|---|---|
19a | 2019.02.19 | Default |
18a | ||
17a | ||
15c | 2016.02.18 | No longer supported |
brms
R library Official Website
Version | Install Date | Notes |
---|---|---|
2.17.0 | 2022.06.10 | Default |
Caret
Version | Install Date | Notes |
---|---|---|
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
Version | Install Date | Notes |
---|---|---|
1.0 | 2021.05.24 | CentOS 7 with Conda |
Chronux
Version | Install Date | Notes |
---|---|---|
2.10 | 2013.02.26 | Current |
CONN
Version | Install Date | Notes |
---|---|---|
19.b | New | |
18.b | ||
17.f | Default |
dcm2nii
Version | Install Date | Notes |
---|---|---|
2013.06.06 | 2014.03.06 | |
2011.11.11 | circa 2011 | Current |
dmctk
Version | Install Date | Notes |
---|---|---|
3.6.0 | 2017.05.17 | Current |
3.6.6 | 2021.02.16 |
DTIprep
Version | Install Date | Notes |
---|---|---|
1.2.4 | 2017.12.21 | |
1.2.9 | 2018.03.20 | Current |
DSI Studio
Please note DSI studio only works with NoMachine
Version | Install Date | Notes |
---|---|---|
"Chen" Release | 2023.07.06 | Current |
dmriprep
Version | Install Date | Notes |
---|---|---|
0.4.0 | 2020.12.10 | Current |
EEGLAB
Version | Install Date | Notes |
---|---|---|
13.1.1b | 2014.01.29 | |
12.0.2.5b | 2013.11.14 | |
11.0.5.4b | 2013.11.14 | |
12.0.0.0b | 2012.12.10 | |
11.0.0.0b | 2012.02.21 | |
10.2.5.8b | 2012.02.21 |
ENIGMA
Version | Install Date | Notes |
---|---|---|
20210422 | 2021.04.22 | Current |
ENIGMA HALFpipe
Version | Install Date | Notes |
---|---|---|
1.1.1 | 2021.08.27 | Current |
FastSurfer
Version | Install Date | Notes |
---|---|---|
202102 | 2021.03.01 | Current |
FIT
Version | Install Date | Notes |
---|---|---|
FITv2.0d | 2021.01.13 | |
FITv2.0e | 2021.01.13 |
FIX
Version | Install Date | Notes |
---|---|---|
1.06.15 | 2021.12.01 |
FMRIprep
Version | Install Date | Notes |
---|---|---|
23.1.3 | 2023.08.22 | Use Apptainer module |
20.2.1 | 2021.05.13 | In Singularity |
20.2.0rc0 | ||
20.1.1 | * known Issue | |
1.4.0 | 2019.01.11 | Default * known Issue |
1.3.2 | 2019.01.11 | * known Issue |
Known issues: please see version history
FreeSurfer
Version | Install Date | Notes |
---|---|---|
7.2.0 | 2021.11.29 | |
7.1.1 | 2021.02.26 | |
6.0.0 | 2017.01.18 | CentOS 6 only |
FSL
Version | Install Date | Notes |
---|---|---|
6.0.4 | 2021.01.25 | new |
6.0.3 | 2021.09.30 | |
6.0.1 | 2019.03.01 | |
6.0.0 | 2018.10.23 | |
5.0.11 | 2018.03.19 | |
5.0.10 | 2017.04.24 | * Known Issue |
5.0.9 | 2015.10.02 | Default |
5.0.8 | 2014.12.03 | |
5.0.7 | 2013.10.17 | |
5.0.6 | 2013.12.18 | (2013.12.18-2014.10.10) |
4.1.9 | 2011.12.01 | |
4.0.4 | circa 2008 |
Known issue: 5.0.10 fsleyes crash on x2go
FSL_MRS
Version | Install Date | Notes |
---|---|---|
2.1.12 | 2023.08.22 | new |
ggseg
Version | Install Date | Notes |
---|---|---|
v1.6.5.9000 | 2023.03.1 |
- Note: ggsegExtra and ggseg3d are also available under these libraries
gift
Version | Install Date | Notes |
---|---|---|
GroupICATv4.0b | 2017.11.14 | |
GroupICATv4.0c | 2021.01.04 |
gradunwarp
Version | Install Date | Notes |
---|---|---|
1.1.0 | 2019.06.04 |
HCP Benchwork
- Note: module name: hcp
Version | Install Date | Notes |
---|---|---|
1.3.2 | 2019.05.22 | New |
1.2.3 | 2018.02.13 | |
1.1.1 | 2016.02.18 | Default |
1.0 | ||
0.84 |
ICA-AROMA
Version | Install Date | Notes |
---|---|---|
0.4.5 | New | |
0.4.1-beta | Default |
- Note: Python 2.7 available for v0.4.5, module name: ica-aroma_py27.
ITKGray
Version | Install Date | Notes |
---|---|---|
080803 | 2009.11.19 | Default |
080128 | 2009.11.13 |
ITKSnap
Version | Install Date | Notes |
---|---|---|
3.4.0.QT4 | 2016.02.24 | Default |
3.6.0.QT4 | 2021.03.02 | |
3.8.0.QT4 | 2021.03.02 | Default |
kwave
Version Number | Install Date | Notes |
---|---|---|
1.3 | 2020.07.20 | Current |
MANGO
Version Number | Install Date | Notes |
---|---|---|
20190905 | Current |
MRIQC
Version Number | Install Date | Notes |
---|---|---|
0.16.1 | 2021.03.08 | Current |
NDATools
Version Number | Install Date | Notes |
---|---|---|
0.2.3 | 2021.03.04 | Current |
OpenSmile
Version Number | Install Date | Notes |
---|---|---|
3.0.0 | 2021.03.23 | Current |
Profumo
Version Number | Install Date | Notes |
---|---|---|
0.11.3 | 2021.06.22 | Current |
RATS
Version Number | Install Date | Notes |
---|---|---|
060419 | 2019.06.04 | Current |
RStan
Version Number | Install Date | Notes |
---|---|---|
4.1.2 | 2022.04.11 | Current |
SPM
Version | Last Patch Applied | Last Checked Date | Notes |
---|---|---|---|
SPM12-standalone | Current | ||
SPM12 | |||
SPM8 | 5236 | 2014.01 | |
SPM5 | Unknown | N/A | No longer supported |
TrackVis/Diffusion Toolkit
Tool | Version Number | Last Checked Date | Notes |
---|---|---|---|
TrackVis | 0.5.2.2 | 2014.03.06 | |
Diffusion Toolkit | 0.6.2.2 | 204.03.06 |
WEKA
Version | Install Date | Notes |
---|---|---|
3.8.1 | ||
3.7.10 | 2014.03.03 | |
3.6.5 | circa 2011.08 |