Hoffman2:Software Tools: Difference between revisions
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==C3D== | ==C3D== | ||
--> | |||
==Caret== | ==Caret== | ||
| Line 100: | Line 100: | ||
| 1.0 || 2021.05.24 || CentOS 7 with Conda | | 1.0 || 2021.05.24 || CentOS 7 with Conda | ||
|} | |} | ||
==Chronux== | ==Chronux== | ||
| Line 126: | Line 127: | ||
| 17.f || || Default | | 17.f || || Default | ||
|} | |} | ||
==dcm2nii== | ==dcm2nii== | ||
| Line 166: | Line 168: | ||
| 1.2.9 || 2018.03.20 || Current | | 1.2.9 || 2018.03.20 || Current | ||
|} | |} | ||
==EEGLAB== | ==EEGLAB== | ||
| Line 201: | Line 204: | ||
| 20210422 || 2021.04.22 || Current | | 20210422 || 2021.04.22 || Current | ||
|} | |} | ||
==ENIGMA HALFpipe== | ==ENIGMA HALFpipe== | ||
| Line 227: | Line 231: | ||
| 202102 || 2021.03.01 || Current | | 202102 || 2021.03.01 || Current | ||
|} | |} | ||
==FIT== | ==FIT== | ||
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| FITv2.0e || 2021.01.13 || | | FITv2.0e || 2021.01.13 || | ||
|} | |} | ||
==FIX== | ==FIX== | ||
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| 1.06.15 || 2021.12.01 || | | 1.06.15 || 2021.12.01 || | ||
|} | |} | ||
==FMRIprep== | ==FMRIprep== | ||
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<div id="Known_issue_2" style="display:inline;">Known issues: please see [https://github.com/nipreps/fmriprep/blob/master/.versions.json version history] </div> | <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== | ==FreeSurfer== | ||
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| 4.0.5 || circa 2008 || | | 4.0.5 || circa 2008 || | ||
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==FSL== | ==FSL== | ||
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<div id="Known_issue_1" style="display:inline;">Known issue: 5.0.10 fsleyes crash on x2go</div> | <div id="Known_issue_1" style="display:inline;">Known issue: 5.0.10 fsleyes crash on x2go</div> | ||
==gift== | ==gift== | ||
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| 1.1.0 || 2019.06.04 || | | 1.1.0 || 2019.06.04 || | ||
|} | |} | ||
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* Note: Python 2.7 available for v0.4.5, module name: ica-aroma_py27. | * 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]] | [[Hoffman2:Software Tools:ica-aroma_py27|Load ica-aroma_py27 module]] | ||
==ITKGray== | ==ITKGray== | ||
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| 080128 || 2009.11.13 || | | 080128 || 2009.11.13 || | ||
|} | |} | ||
==ITKSnap== | ==ITKSnap== | ||
| Line 448: | Line 459: | ||
| 1.3 || 2020.07.20 || Current | | 1.3 || 2020.07.20 || Current | ||
|} | |} | ||
==MANGO== | ==MANGO== | ||
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|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 20190905 || || Current | | 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 | |||
|} | |} | ||
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| 0.2.3 || 2021.03.04 || Current | | 0.2.3 || 2021.03.04 || Current | ||
|} | |} | ||
==OpenSmile== | ==OpenSmile== | ||
| Line 483: | Line 508: | ||
| 3.0.0 || 2021.03.23 || Current | | 3.0.0 || 2021.03.23 || Current | ||
|} | |} | ||
==Profumo== | ==Profumo== | ||
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|} | |} | ||
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==RATS== | ==RATS== | ||
[https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website] | [https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website] | ||
| Line 519: | Line 546: | ||
| 060419 || 2019.06.04 || Current | | 060419 || 2019.06.04 || Current | ||
|} | |} | ||
==SPM== | ==SPM== | ||
Revision as of 00:23, 14 May 2022
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 |
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 |
ENIGMA HALFpipe
| Version | Install Date | Notes |
|---|---|---|
| 1.1.1 | 2021.08.27 | 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 |
|---|---|---|
| 7.2.0 | 2021.11.29 | |
| 7.1.1 | 2021.02.26 | |
| 6.0.0 | 2017.01.18 | CentOS 6 only |
FSL
| 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
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 |
MRIQC
| Version Number | Install Date | Notes |
|---|---|---|
| 0.16.1 | 2021.03.08 | 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 |