Hoffman2:Software Tools: Difference between revisions
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==FIX== | ==FIX== | ||
[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide Official Website] | [https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide Official Website] | ||
[[Hoffman2:Software Tools:Fix|Use Fix in Hoffman]] | |||
{| class="wikitable" | {| class="wikitable" | ||
Revision as of 19:07, 2 December 2021
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.
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 |
C3D
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 |
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 |
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 |
|---|---|---|
| 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 |
|---|---|---|
| 7.1.1 | 2017.01.18 | * CentOS 7 only |
| 6.0.0 | 2017.01.18 | |
| 5.3.0-HCP | 2013.05.13 | |
| 5.3.0 | 2013.05.13 | Default |
| 5.2.0 | 2013.03.27 | |
| 5.1.0 | 2011.11.14 | |
| 5.0.0 | circa 2010 | |
| 4.4.0 | circa 2009 | |
| 4.0.5 | circa 2008 |
FSL
| Version | Install Date | Notes |
|---|---|---|
| 6.0.4 | new | |
| 6.0.3 | ||
| 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
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 |
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 |
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 |