Hoffman2:Software Tools: Difference between revisions
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[[Hoffman2|Back to all things Hoffman2]] | [[Hoffman2|Back to all things Hoffman2]] | ||
There is | 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 | |||
|} | |||
<!-- | |||
==C3D== | |||
--> | |||
==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 | |||
|} | |||
<!-- | |||
|- class="ccn-table-odd" | |||
| 5.3.0-HCP || 2013.05.13 || | |||
|- class="ccn-table-even" style="background-color:#ffffcc;" | |||
| 5.3.0 || 2013.05.13 || Default | |||
|- class="ccn-table-odd" | |||
| 5.2.0 || 2013.03.27 || | |||
|- class="ccn-table-even" | |||
| 5.1.0 || 2011.11.14 || | |||
|- class="ccn-table-odd" | |||
| 5.0.0 || circa 2010 || | |||
|- class="ccn-table-even" | |||
| 4.4.0 || circa 2009 || | |||
|- class="ccn-table-odd" | |||
| 4.0.5 || circa 2008 || | |||
--> | |||
==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 | |||
|} | |||
==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 | |||
|} | |||
<!--==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== | |||
[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 || | |||
|} | |||
<!-- | |||
==Python2.7== | |||
Gentoo Prefix version of Python 2.7. Site packages listed below were installed using pip unless otherwise noted. | |||
Installed by pip unless otherwise noted | |||
===CVXOPT=== | |||
===Cython=== | |||
===Gnuplot=== | |||
===IPython=== | |||
===matplotlib=== | |||
:Installed by Gentoo prefix | |||
===nibabel=== | |||
===nifti=== | |||
===nimfa=== | |||
:Non-negative Matrix Factorization | :Non-negative Matrix Factorization | ||
: | : | ||
:[http://nimfa.biolab.si/ http://nimfa.biolab.si/] | :[http://nimfa.biolab.si/ http://nimfa.biolab.si/] | ||
===nipype=== | |||
===nose=== | |||
===numpy=== | |||
===(p)lsa=== | |||
:(probabilistic) Latent Semantic Analysis. Failed its tests.py though. | :(probabilistic) Latent Semantic Analysis. Failed its tests.py though. | ||
:[http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/ http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/] | :[http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/ http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/] | ||
===pydicom=== | |||
===pygments=== | |||
===PyMF=== | |||
: | :python Matrix Factorization Module. Failed its tests though. | ||
:[http://pymf.googlecode.com http://pymf.googlecode.com] | :[http://pymf.googlecode.com http://pymf.googlecode.com] | ||
===pypr=== | |||
===PyQt4=== | |||
===pytz=== | |||
===pywt=== | |||
===pyximport=== | |||
===scikits=== | |||
===scipy=== | |||
===sklearn=== | |||
===sparsesvd=== | |||
:Singular Value Decomposition. Passed both tests. | :Singular Value Decomposition. Passed both tests. | ||
:[http://pypi.python.org/pypi/sparsesvd http://pypi.python.org/pypi/sparsesvd] | :[http://pypi.python.org/pypi/sparsesvd http://pypi.python.org/pypi/sparsesvd] | ||
===== | ===sphinx=== | ||
===== | ===sympy=== | ||
===== | ===traits=== | ||
===== | ===virtualenv=== | ||
===== | ===xcbgen=== | ||
==GCC== | |||
==LAPACK== | |||
==BLAS== | |||
==GLIB== | |||
==C++== | |||
==CMake== | |||
==CPACK== | |||
==MPI Kmeans== | |||
See this website for how to cite using the MPI Kmeans tool. | |||
[http://mloss.org/software/view/48/] | |||
--> | |||
==External Links== | |||
*[https://www.hoffman2.idre.ucla.edu/software/ Other Hoffman2 Software] |
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 |