Hoffman2:Software Tools: Difference between revisions

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m (update list of software versions)
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|2011.12.21.1014 ||2012.03.19 ||
|2011.12.21.1014 ||2012.03.19 ||
|}
|}


==ANTS==
==ANTS==
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|ants-2.1.0-redhat || 2015.01.23 || Default
|ants-2.1.0-redhat || 2015.01.23 || Default
|}
|}


==ASHS==
==ASHS==
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| Rev-103 || 2016.02.24 || Default
| Rev-103 || 2016.02.24 || Default
|}
|}


==BrainSuite==
==BrainSuite==
[http://brainsuite.org/ Official Website]
[http://brainsuite.org/ Official Website]
{| class="wikitable"  
{| class="wikitable"  
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Version
! 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-even" style="background-color:#ffffcc;"
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 19a || 2019.02.19 || Default
| 19a || 2019.02.19 || Default
|- class="ccn-table-odd"
| 18a ||  ||
|- class="ccn-table-even"
| 17a ||  ||
|- class="ccn-table-odd"
|- class="ccn-table-odd"
| 15c || 2016.02.18 || No longer supported
| 15c || 2016.02.18 || No longer supported
|}
|}


==C3D==
==C3D==


==Caret==
==Caret==
Line 77: Line 86:
| 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
|}
|}


==Chronux==
==Chronux==
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| 2.10 || 2013.02.26 || Current
| 2.10 || 2013.02.26 || Current
|}
|}


==CONN==
==CONN==
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| 17.f || || Default
| 17.f || || Default
|}
|}


==dcm2nii==
==dcm2nii==
Line 112: Line 124:
| 2011.11.11 || circa 2011 || Current
| 2011.11.11 || circa 2011 || Current
|}
|}


==EEGLAB==
==EEGLAB==
Line 134: Line 147:
| 10.2.5.8b || 2012.02.21 ||
| 10.2.5.8b || 2012.02.21 ||
|}
|}


==FMRIprep==
==FMRIprep==
Line 141: Line 155:


{| class="wikitable"  
{| class="wikitable"  
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Version
! 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-even" style="background-color:#E5FFCC;"
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 20.1.1 ||  || New
| 20.2.0rc0 ||  || New
|- class="ccn-table-odd"
|- class="ccn-table-odd"
| 1.4.0 || 2019.01.11 || Default
| 20.1.1 || || * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-even"
|- class="ccn-table-even"
| 1.3.2 || 2019.01.11 ||  
| 1.4.0 || 2019.01.11 || Default  * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-odd"
| 1.3.2 || 2019.01.11 ||   * [[#Known_issue_2 |known Issue ]]
|}
|}
<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==
Line 178: Line 196:
| 4.0.5 || circa 2008 ||
| 4.0.5 || circa 2008 ||
|}
|}


==FSL==
==FSL==
Line 184: Line 203:
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Revision History]
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Revision History]
{| class="wikitable"  
{| class="wikitable"  
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Version
! 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-even" style="background-color:#E5FFCC;"
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 6.0.1 || 2019.03.01 || New
| 6.0.4 || || new
|- class="ccn-table-odd"
| 6.0.3 || ||
|- class="ccn-table-even"
| 6.0.1 || 2019.03.01 ||  
|- class="ccn-table-odd"
|- class="ccn-table-odd"
| 6.0.0 || 2018.10.23 ||  
| 6.0.0 || 2018.10.23 ||  
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| 0.84 ||  ||  
| 0.84 ||  ||  
|}
|}


==ICA-AROMA==
==ICA-AROMA==
{| 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:#E5FFCC;"
| 0.4.5 ||  || New
|- class="ccn-table-odd" style="background-color:#ffffcc;"
| 0.4.1-beta ||  || Default
|}
* Note: Python 2.7 available for v0.4.5, module name: ica-aroma_py27


==ITKGray==
==ITKGray==
[http://vistalab.stanford.edu/newlm/index.php/ItkGray Official Website]
[http://vistalab.stanford.edu/newlm/index.php/ItkGray Official Website]
{| class="wikitable"  
{| class="wikitable"  
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
! class="ccn-table-header"| Notes
Line 244: Line 282:
| 080128 || 2009.11.13 ||
| 080128 || 2009.11.13 ||
|}
|}


==MANGO==
==MANGO==
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 20190905 ||  || Current
|}


==NDATools==
==NDATools==
Line 258: Line 306:
| 0.2.3 || 2021.03.04 || Current
| 0.2.3 || 2021.03.04 || Current
|}
|}


==SPM==
==SPM==
Line 296: Line 345:
[http://www.cs.waikato.ac.nz/ml/weka/ Official Website]
[http://www.cs.waikato.ac.nz/ml/weka/ Official Website]
{| class="wikitable"  
{| class="wikitable"  
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
! class="ccn-table-header"| Notes
Line 367: Line 416:
[http://mloss.org/software/view/48/]
[http://mloss.org/software/view/48/]
-->
-->


==External Links==
==External Links==
*[https://www.hoffman2.idre.ucla.edu/software/ Other Hoffman2 Software]
*[https://www.hoffman2.idre.ucla.edu/software/ Other Hoffman2 Software]

Revision as of 20:40, 22 March 2021

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
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

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

Official Website

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


BrainSuite

Official Website

Version Install Date Notes
19a 2019.02.19 Default
18a
17a
15c 2016.02.18 No longer supported


C3D

Caret

Official Website

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


Chronux

Version Install Date Notes
2.10 2013.02.26 Current


CONN

Official Website

Version Install Date Notes
19.b New
18.b
17.f Default


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
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 pre-requisite modules

Version Install Date Notes
20.2.0rc0 New
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

Official Website

Release Notes

Version Install Date Notes
6.0.0 2017.01.18 New
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

Official Website

Revision History

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


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
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

Official Website

Version Install Date Notes
080803 2009.11.19 Default
080128 2009.11.13


MANGO

Version Number Install Date Notes
20190905 Current


NDATools

Official Website

NDATools

Version Number Install Date Notes
0.2.3 2021.03.04 Current


SPM

Official Website

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

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 Install Date Notes
3.8.1
3.7.10 2014.03.03
3.6.5 circa 2011.08


External Links

Retrieved from "https://www.ccn.ucla.edu/wiki/index.php?title=Hoffman2:Software_Tools&oldid=4489"