Difference between revisions of "Hoffman2:Software Tools"

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==FMRIprep==
 
==FMRIprep==
 
[https://fmriprep.readthedocs.io/en/stable/usage.html Official Website]
 
[https://fmriprep.readthedocs.io/en/stable/usage.html Official Website]
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[[Load modules]]
  
 
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Revision as of 21:31, 22 October 2019

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.


AFNI

Official Webste

Version Install Date Notes
19.0.15 2019.02.20 New
2017.08.09-17.2.07 2017.2.07 Current
2016.10.18-16.3.11 2016.11.20
2011.12.21.1014 2012-03-19

ANTS

Official Website

Version Install Date Notes
ants-2.2.0 2019.03.25 New
ants-2.1.0-redhat 2015.01.23 Current

ASHS

Official Website

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

BrainSuite

Official Website

Version Number Install Date Notes
19a 2019.02.19 Current
15c 2016.02.18

Caret

Official Website

Version Install Date Notes
5.65 (2012.01.27) 2013.07.15 Current, not folded into the main profile


Chronux

Official Website

Version Install Date Notes
2.10 2013.02.26 Current


dcm2nii

Official Website

Version Install Date Notes
2013.06.06 2014.03.06
2011.11.11 circa 2011 Current


EEGLAB

Official Website

Release Notes

Version Install Date Notes
13.1.1b 2014.01.29 Current
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

FMRIprep

Official Website Load modules

Version Number Install Date Notes
1.4.0 2019.01.11
1.3.2 2019.01.11

FreeSurfer

Official Website

Release Notes

Version Install Date Notes
6.0.0 2017.01.18 New
5.3.0-HCP 2013.05.13 Current
5.3.0 2013.05.13
5.3.0 2013.06.18
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

Official Website

Revision History

Version Number Install Date Notes
6.0.1 2019.03.01 New
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 Current
5.0.8 2014.12.03
5.0.7 2013.10.17
5.0.6 2013.12.18 (2013.12.18-2014.10.10)
5.0.5 2013.10.17 (2013.10.17-2013.12.17)
5.0.4 2013.06.18
5.0.2 2013.02.19
5.0.1 2012.10.01
5.0.0 2012.09.14
4.1.9 2011.12.01
4.1.8 circa 2011.06
4.1.7 circa 2011.11
4.1.4 circa 2009
4.1.3 circa 2009
4.1.1 circa 2008
4.1.0 circa 2008
4.0.4 circa 2008
Known issue: 5.0.10 fsleyes crash on x2go


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 Current
1.1.1 2016.02.18

ITKGray

Official Website

Version Number Install Date Notes
080803 2009.11.19 Current
080128 2009.11.13

MRIQC

Official Website

Version Number Install Date Notes
v0.15.1 2019.09.05 Current


SPM

Official Website

Version Last Patch Applied Last Checked Date Notes
SPM8 5236 2014.01 Current
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 Number Install Date Notes
3.7.10 2014.03.03 Current
3.6.5 circa 2011.08