Hoffman2:Software Tools: Difference between revisions

From Center for Cognitive Neuroscience
Jump to navigation Jump to search
No edit summary
 
(24 intermediate revisions by 3 users not shown)
Line 7: Line 7:
Below is a list of the available software tools.  We will do our best to update it as changes are made.
Below is a list of the available software tools.  We will do our best to update it as changes are made.


*Do not load matlab and freesurfer or matlab and RStudio as it will cause errors.


==AFNI==
==AFNI==
Line 73: Line 74:
|}
|}


==BrainAgeR==
[https://github.com/james-cole/brainageR Official Website]
[[Hoffman2:Software Tools:BrainAgeR|Load BrainAgeR module]]
{| 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;"
| 19a || 2019.02.19 || Default
|- class="ccn-table-odd"
| 18a ||  ||
|- class="ccn-table-even"
| 17a ||  ||
|- class="ccn-table-odd"
| 15c || 2016.02.18 || No longer supported
|}
==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==
Line 100: Line 131:
| 1.0 || 2021.05.24 || CentOS 7 with Conda  
| 1.0 || 2021.05.24 || CentOS 7 with Conda  
|}
|}


==Chronux==
==Chronux==
Line 126: Line 158:
| 17.f || || Default
| 17.f || || Default
|}
|}


==dcm2nii==
==dcm2nii==
Line 165: Line 198:
|- class="ccn-table-even"
|- class="ccn-table-even"
| 1.2.9 || 2018.03.20 || Current
| 1.2.9 || 2018.03.20 || Current
|}
==DSI Studio==
[https://dsi-studio.labsolver.org/ Official Website]
===Please note DSI studio only works with NoMachine===
[[Hoffman2:Software Tools:DSI Studio|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| "Chen" Release || 2023.07.06 || Current
|}
==dmriprep==
[https://github.com/nipreps/dmriprep Official Website]
[[Hoffman2:Software Tools:dmriprep|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.4.0 || 2020.12.10 || Current
|}
|}


Line 201: Line 262:
| 20210422 || 2021.04.22 || Current
| 20210422 || 2021.04.22 || Current
|}
|}


==ENIGMA HALFpipe==
==ENIGMA HALFpipe==
Line 227: Line 289:
| 202102 || 2021.03.01 || Current
| 202102 || 2021.03.01 || Current
|}
|}


==FIT==
==FIT==
Line 240: Line 303:
| FITv2.0e || 2021.01.13 ||  
| FITv2.0e || 2021.01.13 ||  
|}
|}


==FIX==
==FIX==
Line 253: Line 317:
| 1.06.15 || 2021.12.01 ||   
| 1.06.15 || 2021.12.01 ||   
|}
|}


==FMRIprep==
==FMRIprep==
Line 263: Line 328:
! 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-odd" style="background-color:#E5FFCC;"
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 23.1.3 ||2023.08.22 || Use Apptainer module
|- class="ccn-table-odd"  
| 20.2.1 ||2021.05.13  || In Singularity
| 20.2.1 ||2021.05.13  || In Singularity
|- class="ccn-table-even"
|- class="ccn-table-even"
Line 287: Line 354:


|- class="ccn-table-even" style="background-color:#E5FFCC;"  
|- class="ccn-table-even" style="background-color:#E5FFCC;"  
| 7.2.0 || 2021.11.29 || *[[Hoffman2:Software Tools:CentOS 7 | CentOS 7 ]] only
| 7.2.0 || 2021.11.29 ||  
|- class="ccn-table-odd"
|- class="ccn-table-odd"
| 7.1.1 || 2021.02.26 || *[[Hoffman2:Software Tools:CentOS 7 | CentOS 7 ]] only
| 7.1.1 || 2021.02.26 ||
|- class="ccn-table-even"   
|- class="ccn-table-even"   
| 6.0.0 || 2017.01.18 ||  
| 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 ||
Line 306: Line 376:
|- class="ccn-table-odd"  
|- class="ccn-table-odd"  
| 4.0.5 || circa 2008 ||
| 4.0.5 || circa 2008 ||
|}
-->
 


==FSL==
==FSL==
Line 318: Line 389:


|- 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 ||  
Line 345: Line 416:
<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>


==FSL_MRS==
[https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/index.html# Official Website]
[https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/changelog.html Revision History]
[[Hoffman2:Software Tools:FSL_MRS|Usage]]
{| 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;"
| 2.1.12 || 2023.08.22|| new
|}
==ggseg==
[https://github.com/ggseg/ggseg Official Website]
[[Hoffman2:Software Tools:ggseg|Load pre-requisite modules]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| v1.6.5.9000 ||  2023.03.1  ||
|- class="ccn-table-even"
|}
* Note: ggsegExtra and ggseg3d are also available under these libraries


==gift==
==gift==
Line 370: Line 473:
| 1.1.0 || 2019.06.04 ||  
| 1.1.0 || 2019.06.04 ||  
|}
|}




Line 376: Line 478:
[https://www.humanconnectome.org/software/connectome-workbench Official Website]
[https://www.humanconnectome.org/software/connectome-workbench Official Website]
* Note: module name: hcp
* Note: module name: hcp
[[Hoffman2:Software Tools:HCPBench|Usage]]
{| class="wikitable"
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Version
Line 391: Line 494:
| 0.84 ||  ||  
| 0.84 ||  ||  
|}
|}


==ICA-AROMA==
==ICA-AROMA==
Line 407: Line 509:
* 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==
Line 419: Line 522:
| 080128 || 2009.11.13 ||
| 080128 || 2009.11.13 ||
|}
|}


==ITKSnap==
==ITKSnap==
Line 446: Line 550:
| 1.3 || 2020.07.20 || Current
| 1.3 || 2020.07.20 || Current
|}
|}


==MANGO==
==MANGO==
Line 455: Line 560:
|- 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
|}
|}


Line 469: Line 586:
| 0.2.3 || 2021.03.04 || Current
| 0.2.3 || 2021.03.04 || Current
|}
|}


==OpenSmile==
==OpenSmile==
Line 480: Line 598:
|- class="ccn-table-odd"
|- class="ccn-table-odd"
| 3.0.0 || 2021.03.23 || Current
| 3.0.0 || 2021.03.23 || Current
|}
==Osprey==
[https://schorschinho.github.io/osprey/]
[[Hoffman2:Software Tools:Osprey|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 2.9.6 || 2025.03.13 || Current
|}
|}


Line 506: Line 635:
|}
|}
-->
-->
==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 516: Line 646:
|- 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
|}
|}


Latest revision as of 18:01, 13 March 2025

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.

  • Do not load matlab and freesurfer or matlab and RStudio as it will cause errors.

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

BrainAgeR

Official Website Load BrainAgeR module

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

brms

R library Official Website

How to load

Version Install Date Notes
2.17.0 2022.06.10 Default


Caret

Official Website

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

How to load

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

Official Website

Load CONN module

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


dmctk

Official Website

Version Install Date Notes
3.6.0 2017.05.17 Current
3.6.6 2021.02.16


DTIprep

Official Website

Version Install Date Notes
1.2.4 2017.12.21
1.2.9 2018.03.20 Current

DSI Studio

Official Website

Please note DSI studio only works with NoMachine

Usage

Version Install Date Notes
"Chen" Release 2023.07.06 Current

dmriprep

Official Website

Usage

Version Install Date Notes
0.4.0 2020.12.10 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


ENIGMA

Official Website

Usage

Version Install Date Notes
20210422 2021.04.22 Current


ENIGMA HALFpipe

Official Website

Usage

Version Install Date Notes
1.1.1 2021.08.27 Current


FastSurfer

Official Website

Usage

Version Install Date Notes
202102 2021.03.01 Current


FIT

Official Website

Version Install Date Notes
FITv2.0d 2021.01.13
FITv2.0e 2021.01.13


FIX

Official Website

Use Fix in Hoffman

Version Install Date Notes
1.06.15 2021.12.01


FMRIprep

Official Website

Load pre-requisite modules

Version Install Date Notes
23.1.3 2023.08.22 Use Apptainer module
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

Official Website

Release Notes

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

Official Website

Revision History

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

FSL_MRS

Official Website

Revision History

Usage

Version Install Date Notes
2.1.12 2023.08.22 new

ggseg

Official Website

Load pre-requisite modules

Version Install Date Notes
v1.6.5.9000 2023.03.1
  • Note: ggsegExtra and ggseg3d are also available under these libraries

gift

Official Website

Version Install Date Notes
GroupICATv4.0b 2017.11.14
GroupICATv4.0c 2021.01.04


gradunwarp

Official Website

Version Install Date Notes
1.1.0 2019.06.04


HCP Benchwork

Official Website

  • Note: module name: hcp

Usage

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.

Load ica-aroma_py27 module


ITKGray

Official Website

Version Install Date Notes
080803 2009.11.19 Default
080128 2009.11.13


ITKSnap

Official Website

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

Official Website

Version Number Install Date Notes
1.3 2020.07.20 Current


MANGO

Version Number Install Date Notes
20190905 Current


MRIQC

Official Website

Version Number Install Date Notes
0.16.1 2021.03.08 Current


NDATools

Official Website

Usage

Version Number Install Date Notes
0.2.3 2021.03.04 Current


OpenSmile

Official Website

Usage

Version Number Install Date Notes
3.0.0 2021.03.23 Current

Osprey

[1] Usage

Version Number Install Date Notes
2.9.6 2025.03.13 Current

Profumo

Official Website

Usage

Version Number Install Date Notes
0.11.3 2021.06.22 Current


RATS

Official Website

Version Number Install Date Notes
060419 2019.06.04 Current

RStan

Official Website

Usage

Version Number Install Date Notes
4.1.2 2022.04.11 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=5529"