Hoffman2:Software Tools

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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

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

ANTS

Official Website

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

Official Website

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

BrainSuite

Official Website

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

Official Website

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

Official Website

Load CONN module

Version	Install Date	Notes
19.b		New
18.b
17.f		Default

dcm2nii

Official Website

Version	Install Date	Notes
2013.06.06	2014.03.06
2011.11.11	circa 2011	Current

dmctk

Official Website

Version	Install Date	Notes
3.6.0	2017.05.17	Current
3.6.6	2021.02.16

DTIprep

Official Website

Version	Install Date	Notes
1.2.4	2017.12.21
1.2.9	2018.03.20	Current

DSI Studio

Official Website

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

Version	Install Date	Notes
"Chen" Release	2023.07.06	Current

EEGLAB

Official Website

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

Official Website

Version	Install Date	Notes
20210422	2021.04.22	Current

ENIGMA HALFpipe

Official Website

Version	Install Date	Notes
1.1.1	2021.08.27	Current

FastSurfer

Official Website

Version	Install Date	Notes
202102	2021.03.01	Current

FIT

Official Website

Version	Install Date	Notes
FITv2.0d	2021.01.13
FITv2.0e	2021.01.13

FIX

Official Website

Use Fix in Hoffman

Version	Install Date	Notes
1.06.15	2021.12.01

FMRIprep

Official Website

Load pre-requisite modules

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

Official Website

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

Official Website

Revision History

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

Official Website

Revision History

Version	Install Date	Notes
2.1.12	2023.08.22	new

ggseg

Official Website

Load pre-requisite modules

Version	Install Date	Notes
v1.6.5.9000	2023.03.1

Note: ggsegExtra and ggseg3d are also available under these libraries

gift

Official Website

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

gradunwarp

Official Website

Version	Install Date	Notes
1.1.0	2019.06.04

HCP Benchwork

Official Website

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.

Load ica-aroma_py27 module

ITKGray

Official Website

Version	Install Date	Notes
080803	2009.11.19	Default
080128	2009.11.13

ITKSnap

Official Website

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

Official Website

Version Number	Install Date	Notes
1.3	2020.07.20	Current

MANGO

Version Number	Install Date	Notes
20190905		Current

MRIQC

Official Website

Version Number	Install Date	Notes
0.16.1	2021.03.08	Current

NDATools

Official Website

Version Number	Install Date	Notes
0.2.3	2021.03.04	Current

OpenSmile

Official Website

Version Number	Install Date	Notes
3.0.0	2021.03.23	Current

Profumo

Official Website

Version Number	Install Date	Notes
0.11.3	2021.06.22	Current

RATS

Official Website

Version Number	Install Date	Notes
060419	2019.06.04	Current

RStan

Official Website

Version Number	Install Date	Notes
4.1.2	2022.04.11	Current

SPM

Official Website

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

Official Website 1

Official Website 2

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

Official Website

Version	Install Date	Notes
3.8.1
3.7.10	2014.03.03
3.6.5	circa 2011.08

External Links

Other Hoffman2 Software

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