Hoffman2:Software Tools: Difference between revisions

Latest revision as of 18:45, 8 April 2026

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

Official Webste

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

@@ Line 7: / Line 7: @@
 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==
@@ 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==
+-->
 ==Caret==
@@ Line 89: / Line 120: @@
 ==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"
+|- class="ccn-table-odd" style="background-color:#E5FFCC;"
-| 1.0 || 2021.05.24 || Conda virtual env with nibabel, nilearn, pydicom, pandas, scikit-learn, scipy
+| 1.0 || 2021.05.24 || CentOS 7 with Conda
 |}
 ==Chronux==
@@ Line 122: / Line 158: @@
 | 17.f || || Default
 |}
 ==dcm2nii==
@@ Line 161: / Line 198: @@
 |- 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
 |}
@@ Line 197: / Line 262: @@
 | 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==
@@ Line 210: / Line 289: @@
 | 202102 || 2021.03.01 || Current
 |}
 ==FIT==
@@ Line 222: / Line 302: @@
 |- 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 ||
 |}
@@ Line 234: / Line 328: @@
 ! class="ccn-table-header"| Install Date
 ! class="ccn-table-header"| Notes
-|- class="ccn-table-odd" style="background-color:#E5FFCC;"
+|- class="ccn-table-odd"
+| 25.1.3 ||2025.07.27  || In Apptainer
+|- class="ccn-table-even"
+| 24.1.1 ||2024.11.01  || In Apptainer
+|- class="ccn-table-odd"
+| 23.2.0 ||2024.03.12  || In Apptainer
+|- class="ccn-table-even" style="background-color:#E5FFCC;"
+| 23.1.3 ||2023.08.22 || Use Apptainer module
+|- class="ccn-table-odd"
 | 20.2.1 ||2021.05.13  || In Singularity
 |- class="ccn-table-even"
@@ Line 257: / Line 359: @@
 ! class="ccn-table-header" | Notes
-|- class="ccn-table-odd" style="background-color:#E5FFCC;"
+|- class="ccn-table-even" style="background-color:#E5FFCC;"
-| 7.1.1 || 2017.01.18 || *[[Hoffman2:Software Tools:CentOS 7 | CentOS 7 ]] only
+| 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 ||
+| 6.0.0 || 2017.01.18 || CentOS 6 only
+|}
+<!--
 |- class="ccn-table-odd"
 | 5.3.0-HCP || 2013.05.13 ||
@@ Line 275: / Line 382: @@
 |- class="ccn-table-odd"
 | 4.0.5 || circa 2008 ||
-|}
+-->
 ==FSL==
@@ Line 287: / Line 395: @@
 |- class="ccn-table-even" style="background-color:#E5FFCC;"
-| 6.0.4 || || new
+| 6.0.4 || 2021.01.25|| new
 |- class="ccn-table-odd"
-| 6.0.3 || ||
+| 6.0.3 || 2021.09.30||
 |- class="ccn-table-even"
 | 6.0.1 || 2019.03.01 ||
@@ Line 314: / Line 422: @@
 <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==
@@ Line 339: / Line 479: @@
 | 1.1.0 || 2019.06.04 ||
 |}
@@ Line 345: / Line 484: @@
 [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
@@ Line 360: / Line 500: @@
 | 0.84 ||  ||
 |}
 ==ICA-AROMA==
@@ Line 376: / Line 515: @@
 * 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==
@@ Line 388: / Line 528: @@
 | 080128 || 2009.11.13 ||
 |}
 ==ITKSnap==
@@ Line 415: / Line 556: @@
 | 1.3 || 2020.07.20 || Current
 |}
 ==MANGO==
@@ Line 424: / Line 566: @@
 |- 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
 |}
@@ Line 438: / Line 592: @@
 | 0.2.3 || 2021.03.04 || Current
 |}
 ==OpenSmile==
@@ Line 449: / Line 604: @@
 |- class="ccn-table-odd"
 | 3.0.0 || 2021.03.23 || Current
+|}
+==Osprey==
+[https://schorschinho.github.io/osprey/]
+[[Hoffman2:Software Tools:Osprey|Usage]]
+{| class="wikitable"
+! class="ccn-table-header"| Version Number
+! class="ccn-table-header"| Install Date
+! class="ccn-table-header"| Notes
+|- class="ccn-table-odd"
+| 2.9.6 || 2025.03.13 || Current
 |}
@@ Line 464: / Line 630: @@
 |}
-==Pytorch==
+<!--==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"
+|- 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]
@@ Line 483: / Line 652: @@
 |- 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
 |}

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

Version	Install Date	Notes
20180720	2018.07.20	New
2017-02	2017.06.08
Rev-103	2016.02.24	Default

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

Version	Install Date	Notes
25.1.3	2025.07.27	In Apptainer
24.1.1	2024.11.01	In Apptainer
23.2.0	2024.03.12	In Apptainer
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

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

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

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

Version	Last Patch Applied	Last Checked Date	Notes
SPM12-standalone			Current
SPM12
SPM8	5236	2014.01
SPM5	Unknown	N/A	No longer supported

Version	Install Date	Notes
GroupICATv4.0b	2017.11.14
GroupICATv4.0c	2021.01.04

Hoffman2:Software Tools: Difference between revisions

Latest revision as of 18:45, 8 April 2026

AFNI

ANTS

ASHS

BrainSuite

BrainAgeR

brms

Caret

ccn_py37

Chronux

CONN

dcm2nii

dmctk

DTIprep

DSI Studio

Please note DSI studio only works with NoMachine

dmriprep

EEGLAB

ENIGMA

ENIGMA HALFpipe

FastSurfer

FIT

FIX

FMRIprep

FreeSurfer

FSL

FSL_MRS

ggseg

gift

gradunwarp

HCP Benchwork

ICA-AROMA

ITKGray

ITKSnap

kwave

MANGO

MRIQC

NDATools

OpenSmile

Osprey

Profumo

RATS

RStan

SPM

TrackVis/Diffusion Toolkit

WEKA

External Links

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