File:Matlab install.png

2024-12-03T17:57:23Z

Jonathan:

Matlab licenses

2024-12-03T17:56:08Z

Jonathan: /* Access the Portal */

= Getting Your Matlab License =

== Access the Portal ==
# Go to [https://www.mathworks.com/academia/tah-portal/ucla-31454052.html MathWorks Portal]
# Click "Sign In" (top right)
# Use your mednet login

[[File:Matlab_login.png|center|700px|Matlab Login Page]]

== Select Your License ==
# Find the "Licenses" section
# Choose your license type
# Accept the license agreement

== Download and Install ==
# Click "Download"
# Select your operating system
# Follow installation prompts
# Login with your Mathworks account and the license will be attached during the installation

== Need Help? ==
Contact ccnsupport@g.ucla.edu

[[Category:Software]]
[[Category:Licenses]]

File:Matlab login.png

2024-12-03T17:53:26Z

Jonathan:

Matlab licenses

2024-12-03T17:50:06Z

Jonathan: Created page with "= Getting Your Matlab License = == Access the Portal == # Go to [https://www.mathworks.com/academia/tah-portal/ucla-31454052.html MathWorks Portal] # Click "Sign In" (top right) # Use your mednet login == Select Your License == # Find the "Licenses" section # Choose your license type # Accept the license agreement == Download and Install == # Click "Download" # Select your operating system # Follow installation prompts # Login with your Mathworks account and the li..."

= Getting Your Matlab License =

== Access the Portal ==
# Go to [https://www.mathworks.com/academia/tah-portal/ucla-31454052.html MathWorks Portal]
# Click "Sign In" (top right)
# Use your mednet login

== Select Your License ==
# Find the "Licenses" section
# Choose your license type
# Accept the license agreement

== Download and Install ==
# Click "Download"
# Select your operating system
# Follow installation prompts
# Login with your Mathworks account and the license will be attached during the installation

== Need Help? ==
Contact ccnsupport@g.ucla.edu

[[Category:Software]]
[[Category:Licenses]]

Licensing

2024-12-03T17:47:03Z

Jonathan:

[[Matlab licenses]]

2023-12-13T15:49:59Z

Jonathan:

===DSI Studio===

Log in via NoMachine

module load singularity
singularity exec dsistudio_2023.07.08.sif dsi_studio

2023-08-22T18:12:11Z

Jonathan: Created blank page

Hoffman2:Software Tools

2023-08-22T18:11:40Z

Jonathan: /* FSL_MRS */

[[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
|}

==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
{| 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
|}



==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

2023-08-22T17:16:04Z

Jonathan:

[[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
|}

==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]
{| 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
{| 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
|}



==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

2023-08-22T17:10:12Z

Jonathan: /* 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
|}

==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>

==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
{| 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
|}



==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 maintenance and Issues

2023-04-06T16:56:04Z

Jonathan: /* Issues and Solutions */

== 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:Software Tools:ggseg

2023-03-10T01:03:31Z

Jonathan: /* From a Hoffman2 node */

==From a Hoffman2 node==

Load the required modules:
<pre>
module load R/4.2.2
module load anaconda3/2022.05
module load freesurfer/7.3.2
module load proj/7.1.1
module load gdal/3.1.3</pre>

Add the path
<pre>export PATH=$PATH:/u/project/CCN/apps/conda/rh7/R4.2.2_ggseg:/u/project/CCN/apps/R_libs/rh7/4.2.2_ggseg</pre>

Activate the conda environment:
<pre>conda activate /u/project/CCN/apps/conda/rh7/R4.2.2_ggseg</pre>

Launch R with the command "R" and enter the following:
<pre>.libPaths("/u/project/CCN/apps/R_libs/rh7/4.2.2_ggseg")</pre>

Load the library in R
<pre>library(ggseg)</pre>
<pre>library(ggseg3d)</pre>
<pre>library(ggsegExtra)</pre>