Hoffman2:Software Tools: Difference between revisions
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(Updating versions listed and changing to table layout.) |
(Re-sorted tools and finished switch to table method of listing.) |
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==List of Tools== | ==List of Tools== | ||
Under Construction... | Under Construction... | ||
=== | |||
[http:// | |||
===AFNI=== | |||
[http:// | [http://afni.nimh.nih.gov/afni/ Official Webste] | ||
{| class="wikitable" | |||
! class="ccn-table-header" | Version | |||
! class="ccn-table-header" | Install Date | |||
! class="ccn-table-header" | Notes | |||
|- class="ccn-table-odd" | |||
| 2011_12_21_1014 || circa 2012.03 || Current | |||
|} | |||
===BrainSuite=== | |||
[http://brainsuite.org/ Official Website] | |||
{| class="wikitable" | {| class="wikitable" | ||
! class="ccn-table-header"| Version Number | ! class="ccn-table-header"| Version Number | ||
! class="ccn-table-header"| Install Date | ! class="ccn-table-header"| Install Date | ||
! class="ccn-table-header"| Notes | |||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| | | 13a4 || 2014.03.05 || Current | ||
|- class="ccn-table- | |} | ||
| | |||
|-class="ccn-table-odd" | |||
| 5. | ===Caret=== | ||
|- class="ccn-table- | [http://brainvis.wustl.edu/wiki/index.php/Caret:About Official Website] | ||
| | {| class="wikitable" | ||
! class="ccn-table-header" | Version | |||
! class="ccn-table-header" | Install Date | |||
! class="ccn-table-header" | Notes | |||
|- class="ccn-table-odd" | |||
| 5.65 (2012.01.27) || 2013.07.15 || Current, not folded into the main profile | |||
|} | |||
===Chronux=== | |||
[http://www.chronux.org Official Website] | |||
{| class="wikitable" | |||
! class="ccn-table-header" | Version | |||
! class="ccn-table-header" | Install Date | |||
! class="ccn-table-header" | Notes | |||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| | | 2.10 || 2013.02.26 || Current | ||
|- class="ccn-table- | |} | ||
| | |||
===dcm2nii=== | |||
[http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html Official Website] | |||
{| class="wikitable" | |||
! class="ccn-table-header" | Version | |||
! class="ccn-table-header" | Install Date | |||
! class="ccn-table-header" | Notes | |||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| | | 2013.06.06 || 2014.03.06 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| | | 2011.11.11 || circa 2011 || Current | ||
|} | |||
===EEGLAB=== | |||
[http://sccn.ucsd.edu/eeglab/ Official Website] | |||
[http://sccn.ucsd.edu/wiki/EEGLAB_revision_history Release Notes] | |||
{| class="wikitable" | |||
! class="ccn-table-header" | Version | |||
! class="ccn-table-header" | Install Date | |||
! class="ccn-table-header" | Notes | |||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| | | 13.1.1b || 2014.01.29 || Current | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| | | 12.0.2.5b || 2013.11.14 || | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| | | 11.0.5.4b || 2013.11.14 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| | | 12.0.0.0b || 2012.12.10 || | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| | | 11.0.0.0b || 2012.02.21 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| | | 10.2.5.8b || 2012.02.21 || | ||
|} | |} | ||
===FreeSurfer=== | ===FreeSurfer=== | ||
Line 49: | Line 94: | ||
[http://freesurfer.net/fswiki/ReleaseNotes Release Notes] | [http://freesurfer.net/fswiki/ReleaseNotes Release Notes] | ||
{| class="wikitable" | {| class="wikitable" | ||
! class="ccn-table-header" | Version | ! 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-odd" | |- class="ccn-table-odd" | ||
| 5.3.0 || 2013.06.18 | | 5.3.0 || 2013.06.18 || Current | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 5.2.0 || 2013.03.27 | | 5.2.0 || 2013.03.27 || | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 5.1.0 || 2011.11.14 | | 5.1.0 || 2011.11.14 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 5.0.0 || circa 2010 | | 5.0.0 || circa 2010 || | ||
|- class="ccn-table-odd" | |- class="ccn-table-odd" | ||
| 4.4.0 || circa 2009 | | 4.4.0 || circa 2009 || | ||
|- class="ccn-table-even" | |- class="ccn-table-even" | ||
| 4.0.5 || circa 2008 | | 4.0.5 || circa 2008 || | ||
|} | |} | ||
=== | ===FSL=== | ||
[http:// | [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website] | ||
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Revision History] | |||
{| class="wikitable" | |||
! class="ccn-table-header"| Version Number | |||
! class="ccn-table-header"| Install Date | |||
! class="ccn-table-header"| Notes | |||
|- class="ccn-table-odd" | |||
| 5.0.6 || 2013.12.18 || Current | |||
|- class="ccn-table-even" | |||
| 5.0.5 || 2013.10.17 || | |||
|-class="ccn-table-odd" | |||
| 5.0.4 || 2013.06.18 || | |||
|- class="ccn-table-even" | |||
| 5.0.2 || 2013.02.19 || | |||
|- class="ccn-table-odd" | |||
| 5.0.1 || 2012.10.01 || | |||
|- class="ccn-table-even" | |||
| 5.0.0 || 2012.09.14 || | |||
|- class="ccn-table-odd" | |||
| 4.1.9 || 2011.12.01 || | |||
|- class="ccn-table-even" | |||
| 4.1.8 || circa 2011.06 || | |||
|- class="ccn-table-odd" | |||
| 4.1.7 || circa 2011.11 || | |||
|- class="ccn-table-even" | |||
| 4.1.4 || circa 2009 || | |||
|- class="ccn-table-odd" | |||
| 4.1.3 || circa 2009 || | |||
|- class="ccn-table-even" | |||
| 4.1.1 || circa 2008 || | |||
|- class="ccn-table-odd" | |||
| 4.1.0 || circa 2008 || | |||
|- class="ccn-table-even" | |||
| 4.0.4 || circa 2008 || | |||
|} | |||
===GCC=== | ===GCC=== |
Revision as of 20:40, 6 March 2014
There is an FMRI 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 setup your bash profile properly.
Below is a list of the available software tools. We will do our best to update it in real-time.
List of Tools
Under Construction...
AFNI
Version | Install Date | Notes |
---|---|---|
2011_12_21_1014 | circa 2012.03 | Current |
BrainSuite
Version Number | Install Date | Notes |
---|---|---|
13a4 | 2014.03.05 | Current |
Caret
Version | Install Date | Notes |
---|---|---|
5.65 (2012.01.27) | 2013.07.15 | Current, not folded into the main profile |
Chronux
Version | Install Date | Notes |
---|---|---|
2.10 | 2013.02.26 | Current |
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 | 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 |
FreeSurfer
Version | Install Date | Notes |
---|---|---|
5.3.0 | 2013.06.18 | Current |
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 |
---|---|---|
5.0.6 | 2013.12.18 | Current |
5.0.5 | 2013.10.17 | |
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 |
GCC
LAPACK
BLAS
GLIB
C++
CMake
CPACK
MPI Kmeans
See this website for how to cite using the MPI Kmeans tool. [1]
Python2.7
Packages
CVXOPT
Cython
Gnuplot
IPython
matplotlib
nibabel
nifti
nimfa
- Non-negative Matrix Factorization
- http://nimfa.biolab.si/
nipype
nose
numpy
(p)lsa
- (probabilistic) Latent Semantic Analysis. Failed its tests.py though.
pydicom
pygments
PyMF
- Python Matrix Factorization Module. Failed its tests though.
pypr
PyQt4
pytz
pywt
pyximport
scikits
scipy
sklearn
sparsesvd
- Singular Value Decomposition. Passed both tests.