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
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
ants-2.3.1 |
|
New
|
ants-2.2.0 |
2019.03.25 |
|
ants-2.1.0-redhat |
2015.01.23 |
Default
|
ASHS
Official Website
20180720 |
2018.07.20 |
New
|
2017-02 |
2017.06.08 |
|
Rev-103 |
2016.02.24 |
Default
|
BrainSuite
Official Website
19a |
2019.02.19 |
Default
|
18a |
|
|
17a |
|
|
15c |
2016.02.18 |
No longer supported
|
BrainAgeR
Official Website
Load BrainAgeR module
19a |
2019.02.19 |
Default
|
18a |
|
|
17a |
|
|
15c |
2016.02.18 |
No longer supported
|
brms
R library Official Website
How to load
2.17.0 |
2022.06.10 |
Default
|
Caret
Official Website
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
How to load
1.0 |
2021.05.24 |
CentOS 7 with Conda
|
Chronux
CONN
Official Website
Load CONN module
19.b |
|
New
|
18.b |
|
|
17.f |
|
Default
|
dcm2nii
Official Website
2013.06.06 |
2014.03.06 |
|
2011.11.11 |
circa 2011 |
Current
|
dmctk
Official Website
3.6.0 |
2017.05.17 |
Current
|
3.6.6 |
2021.02.16
|
DTIprep
Official Website
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
"Chen" Release |
2023.07.06 |
Current
|
EEGLAB
Official Website
Release 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
Usage
20210422 |
2021.04.22 |
Current
|
ENIGMA HALFpipe
Official Website
Usage
FastSurfer
Official Website
Usage
202102 |
2021.03.01 |
Current
|
FIT
Official Website
FITv2.0d |
2021.01.13 |
|
FITv2.0e |
2021.01.13 |
|
FIX
Official Website
Use Fix in Hoffman
FMRIprep
Official Website
Load pre-requisite modules
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
|
FreeSurfer
Official Website
Release 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
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
Usage
ggseg
Official Website
Load pre-requisite modules
- Note: ggsegExtra and ggseg3d are also available under these libraries
gift
Official Website
GroupICATv4.0b |
2017.11.14 |
|
GroupICATv4.0c |
2021.01.04 |
|
gradunwarp
Official Website
HCP Benchwork
Official Website
Usage
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
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
080803 |
2009.11.19 |
Default
|
080128 |
2009.11.13 |
|
ITKSnap
Official Website
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
MANGO
MRIQC
Official Website
0.16.1 |
2021.03.08 |
Current
|
NDATools
Official Website
Usage
OpenSmile
Official Website
Usage
Profumo
Official Website
Usage
0.11.3 |
2021.06.22 |
Current
|
RATS
Official Website
060419 |
2019.06.04 |
Current
|
RStan
Official Website
Usage
SPM
Official Website
SPM12-standalone |
|
|
Current
|
SPM12 |
|
|
|
SPM8 |
5236 |
2014.01 |
|
SPM5 |
Unknown |
N/A |
No longer supported
|
TrackVis/Diffusion Toolkit
Official Website 1
Official Website 2
TrackVis |
0.5.2.2 |
2014.03.06 |
|
Diffusion Toolkit |
0.6.2.2 |
204.03.06 |
|
WEKA
Official Website
3.8.1 |
|
|
3.7.10 |
2014.03.03 |
|
3.6.5 |
circa 2011.08 |
|
External Links