Hoffman2:Software Tools: Difference between revisions
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==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== | ==C3D== | ||
--> | |||
==Caret== | ==Caret== | ||
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|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5.65 (2012.01.27) || 2013.07.15 || Default, not folded into the main profile | | 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 | |||
[[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" style="background-color:#E5FFCC;" | |||
| 1.0 || 2021.05.24 || CentOS 7 with Conda | |||
|} | |} | ||
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| 17.f || || Default | | 17.f || || Default | ||
|} | |} | ||
==dcm2nii== | ==dcm2nii== | ||
Line 153: | Line 181: | ||
| 1.2.9 || 2018.03.20 || Current | | 1.2.9 || 2018.03.20 || Current | ||
|} | |} | ||
==EEGLAB== | ==EEGLAB== | ||
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| 20210422 || 2021.04.22 || Current | | 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== | ==FastSurfer== | ||
[https://github.com/Deep-MI/FastSurfer/ Official Website] | [https://github.com/Deep-MI/FastSurfer/ Official Website] | ||
[[Hoffman2:Software Tools:FastSurfer|Usage]] | |||
{| class="wikitable" | {| class="wikitable" | ||
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|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| FITv2.0e || 2021.01.13 || | | 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 || | |||
|} | |} | ||
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[https://fmriprep.readthedocs.io/en/stable/usage.html Official Website] | [https://fmriprep.readthedocs.io/en/stable/usage.html Official Website] | ||
[[Hoffman2:Software Tools: FMRIprep|Load pre-requisite modules]] | [[Hoffman2:Software Tools:FMRIprep|Load pre-requisite modules]] | ||
{| class="wikitable" | {| class="wikitable" | ||
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! class="ccn-table-header"| Install Date | ! class="ccn-table-header"| Install Date | ||
! class="ccn-table-header"| Notes | ! class="ccn-table-header"| Notes | ||
|- class="ccn-table- | |- class="ccn-table-odd" style="background-color:#E5FFCC;" | ||
| 20.2.0rc0 || || | | 20.2.1 ||2021.05.13 || In Singularity | ||
|- class="ccn-table-even" | |||
| 20.2.0rc0 || || | |||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 20.1.1 || || * [[#Known_issue_2 |known Issue ]] | | 20.1.1 || || * [[#Known_issue_2 |known Issue ]] | ||
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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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|- class="ccn-table-even" style="background-color:#E5FFCC;" | |- class="ccn-table-even" style="background-color:#E5FFCC;" | ||
| 6.0.0 || 2017.01.18 || | | 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 || CentOS 6 only | |||
|} | |||
<!-- | |||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5.3.0-HCP || 2013.05.13 || | | 5.3.0-HCP || 2013.05.13 || | ||
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|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 4.0.5 || circa 2008 || | | 4.0.5 || circa 2008 || | ||
--> | |||
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|- class="ccn-table-even" style="background-color:#E5FFCC;" | |- class="ccn-table-even" style="background-color:#E5FFCC;" | ||
| 6.0.4 || || new | | 6.0.4 || 2021.01.25|| new | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 6.0.3 || || | | 6.0.3 || 2021.09.30|| | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 6.0.1 || 2019.03.01 || | | 6.0.1 || 2019.03.01 || | ||
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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== | ||
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| 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== | ||
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| 3.0.0 || 2021.03.23 || Current | | 3.0.0 || 2021.03.23 || Current | ||
|} | |} | ||
==Profumo== | ==Profumo== | ||
[https://git.fmrib.ox.ac.uk/samh/profumo Official Website] | [https://git.fmrib.ox.ac.uk/samh/profumo Official Website] | ||
[[Hoffman2:Software Tools: | [[Hoffman2:Software Tools:Profumo|Usage]] | ||
{| class="wikitable" | {| class="wikitable" | ||
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| 0.11.3 || 2021.06.22 || Current | | 0.11.3 || 2021.06.22 || Current | ||
|} | |} | ||
<!--==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" style="background-color:#E5FFCC;" | |||
| 1.8.0 || 2021.04.20 || CentOS 7 and GPU | |||
|} | |||
--> | |||
==RATS== | ==RATS== | ||
[https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website] | [https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website] | ||
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|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 060419 || 2019.06.04 || Current | | 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 | |||
|} | |} | ||
Revision as of 23:20, 26 July 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 |
brms
R library Official Website
Version | Install Date | Notes |
---|---|---|
2.17.0 | 2022.06.10 | Default |
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 |
RStan
Version Number | Install Date | Notes |
---|---|---|
4.1.2 | 2022.04.11 | 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 |