Hoffman2:Software Tools: Difference between revisions
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! 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;" | ||
|19.0.15 || 2019.02.20 || | |20.1.00 || || New | ||
|- class="ccn-table- | |- class="ccn-table-odd" | ||
| | |19.0.15 || 2019.02.20 || | ||
|- class="ccn-table- | |- class="ccn-table-even" style="background-color:#ffffcc;" | ||
| | |17.2.07 || 2017.02.07 || Default | ||
|- class="ccn-table- | |- class="ccn-table-odd" | ||
|2011.12.21.1014 ||2012 | |16.3.1 || 2016.11.20 || | ||
|- class="ccn-table-even"" | |||
|2011.12.21.1014 ||2012.03.19 || | |||
|} | |} | ||
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! 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;" | ||
|ants-2.2.0 || 2019.03.25 || | |ants-2.3.1 || || New | ||
|- class="ccn-table- | |- class="ccn-table-odd" | ||
|ants-2.1.0-redhat || 2015.01.23 || | |ants-2.2.0 || 2019.03.25 || | ||
|- class="ccn-table-even" style="background-color:#ffffcc;" | |||
|ants-2.1.0-redhat || 2015.01.23 || Default | |||
|} | |} | ||
Line 43: | Line 47: | ||
! 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;" | ||
| 20180720 || 2018.07.20 || | | 20180720 || 2018.07.20 || New | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 2017-02 || 2017.06.08 || | | 2017-02 || 2017.06.08 || | ||
|- class="ccn-table-odd" style="background-color:#ffffcc;" | |- class="ccn-table-odd" style="background-color:#ffffcc;" | ||
| Rev-103 || 2016.02.24 || | | Rev-103 || 2016.02.24 || Default | ||
|} | |} | ||
Line 57: | Line 61: | ||
! 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 || | | 19a || 2019.02.19 || Default | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 15c || 2016.02.18 || | | 15c || 2016.02.18 || No longer supported | ||
|} | |} | ||
==C3D== | |||
==Caret== | ==Caret== | ||
Line 69: | Line 75: | ||
! class="ccn-table-header" | Notes | ! class="ccn-table-header" | Notes | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5.65 (2012.01.27) || 2013.07.15 || | | 5.65 (2012.01.27) || 2013.07.15 || Default, not folded into the main profile | ||
|} | |} | ||
==Chronux== | ==Chronux== | ||
{| class="wikitable" | {| class="wikitable" | ||
! class="ccn-table-header" | Version | ! class="ccn-table-header" | Version | ||
Line 83: | Line 87: | ||
|} | |} | ||
==CONN== | |||
[https://web.conn-toolbox.org/ Official Website] | |||
{| 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;" | |||
| 19.b || || New | |||
|- class="ccn-table-odd" | |||
| 18.b || || | |||
|- class="ccn-table-even" style="background-color:#ffffcc;" | |||
| 17.f || || Default | |||
|} | |||
==dcm2nii== | ==dcm2nii== | ||
Line 95: | Line 112: | ||
| 2011.11.11 || circa 2011 || Current | | 2011.11.11 || circa 2011 || Current | ||
|} | |} | ||
==EEGLAB== | ==EEGLAB== | ||
Line 106: | Line 122: | ||
! class="ccn-table-header" | Notes | ! class="ccn-table-header" | Notes | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 13.1.1b || 2014.01.29 || | | 13.1.1b || 2014.01.29 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 12.0.2.5b || 2013.11.14 || | | 12.0.2.5b || 2013.11.14 || | ||
Line 129: | Line 145: | ||
! 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;" | ||
| 1. | | 20.1.1 || || New | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 1.3.2|| 2019.01.11 || | | 1.4.0 || 2019.01.11 || Default | ||
|- class="ccn-table-even" | |||
| 1.3.2 || 2019.01.11 || | |||
|} | |} | ||
Line 145: | Line 163: | ||
|- class="ccn-table-even" style="background-color:#E5FFCC;" | |- class="ccn-table-even" style="background-color:#E5FFCC;" | ||
| 6.0.0 || 2017.01.18 || New | | 6.0.0 || 2017.01.18 || New | ||
|- class="ccn-table-odd | |- class="ccn-table-odd" | ||
| 5.3.0-HCP || 2013.05.13 || | | 5.3.0-HCP || 2013.05.13 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" style="background-color:#ffffcc;" | ||
| 5.3.0 || 2013.05.13 || | | 5.3.0 || 2013.05.13 || Default | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5. | | 5.2.0 || 2013.03.27 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 5. | | 5.1.0 || 2011.11.14 || | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5. | | 5.0.0 || circa 2010 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| | | 4.4.0 || circa 2009 || | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 4.0.5 || circa 2008 || | | 4.0.5 || circa 2008 || | ||
|} | |} | ||
Line 180: | Line 196: | ||
| 5.0.10 || 2017.04.24 || * [[#Known_issue_1 |Known Issue ]] | | 5.0.10 || 2017.04.24 || * [[#Known_issue_1 |Known Issue ]] | ||
|- class="ccn-table-even" style="background-color:#ffffcc;" | |- class="ccn-table-even" style="background-color:#ffffcc;" | ||
| 5.0.9 || 2015.10.02 || | | 5.0.9 || 2015.10.02 || Default | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5.0.8 || 2014.12.03 || | | 5.0.8 || 2014.12.03 || | ||
Line 187: | Line 203: | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5.0.6 || 2013.12.18 || (2013.12.18-2014.10.10) | | 5.0.6 || 2013.12.18 || (2013.12.18-2014.10.10) | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 4.1.9 || 2011.12.01 || | | 4.1.9 || 2011.12.01 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 4.0.4 || circa 2008 || | | 4.0.4 || circa 2008 || | ||
Line 227: | Line 221: | ||
|- class="ccn-table-even" style="background-color:#E5FFCC;" | |- class="ccn-table-even" style="background-color:#E5FFCC;" | ||
| 1.3.2 || 2019.05.22 || New | | 1.3.2 || 2019.05.22 || New | ||
|- class="ccn-table-odd" style="background-color:#ffffcc;" | |- class="ccn-table-odd" | ||
| 1. | | 1.2.3 || 2018.02.13 || | ||
|- class="ccn-table-even" style="background-color:#ffffcc;" | |||
| 1.1.1 || 2016.02.18 || Default | |||
|- class="ccn-table-odd" | |||
| 1.0 || || | |||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| | | 0.84 || || | ||
|} | |} | ||
==ICA-AROMA== | |||
==ITKGray== | ==ITKGray== | ||
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! class="ccn-table-header"| Notes | ! class="ccn-table-header"| Notes | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 080803 || 2009.11.19 || | | 080803 || 2009.11.19 || Default | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 080128 || 2009.11.13 || | | 080128 || 2009.11.13 || | ||
|} | |} | ||
==MANGO== | |||
<!--==MRIQC== | <!--==MRIQC== | ||
Line 262: | Line 264: | ||
! class="ccn-table-header"| Last Checked Date | ! class="ccn-table-header"| Last Checked Date | ||
! class="ccn-table-header"| Notes | ! class="ccn-table-header"| Notes | ||
|- class="ccn-table-odd" style="background-color:#E5FFCC;" | |||
| SPM12-standalone || || || Current | |||
|- class="ccn-table-even" | |||
| SPM12 || || || | |||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| SPM8 || 5236 || 2014.01 || | | SPM8 || 5236 || 2014.01 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| SPM5 || Unknown || N/A || No longer supported | | SPM5 || Unknown || N/A || No longer supported | ||
Line 291: | Line 297: | ||
! 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;" | |||
| 3.8.1 || || | |||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 3.7.10 || 2014.03.03 || | | 3.7.10 || 2014.03.03 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 3.6.5 || circa 2011.08 || | | 3.6.5 || circa 2011.08 || | ||
|} | |} | ||
<!-- | <!-- | ||
==Python2.7== | ==Python2.7== |
Revision as of 14:35, 31 July 2020
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 Number | Install Date | Notes |
---|---|---|
19a | 2019.02.19 | Default |
15c | 2016.02.18 | No longer supported |
C3D
Caret
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
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 |
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 |
FMRIprep
Version Number | Install Date | Notes |
---|---|---|
20.1.1 | New | |
1.4.0 | 2019.01.11 | Default |
1.3.2 | 2019.01.11 |
FreeSurfer
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
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 | 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
- 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
ITKGray
Version Number | Install Date | Notes |
---|---|---|
080803 | 2009.11.19 | Default |
080128 | 2009.11.13 |
MANGO
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 Number | Install Date | Notes |
---|---|---|
3.8.1 | ||
3.7.10 | 2014.03.03 | |
3.6.5 | circa 2011.08 |