Difference between revisions of "Hoffman2:Software Tools"

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(Updating versions listed and changing to table layout.)
(Re-sorted tools and finished switch to table method of listing.)
Line 8: Line 8:
 
==List of Tools==
 
==List of Tools==
 
Under Construction...
 
Under Construction...
===FSL===
+
 
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]
+
 
+
===AFNI===
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Revision History]
+
[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"
| 5.0.6 || 2013.12.18
+
| 13a4 || 2014.03.05 || Current
|- class="ccn-table-even"
+
|}
| 5.0.5 || 2013.10.17
+
 
|-class="ccn-table-odd"
+
 
| 5.0.4 || 2013.06.18
+
===Caret===
|- class="ccn-table-even"
+
[http://brainvis.wustl.edu/wiki/index.php/Caret:About Official Website]
| 5.0.2 || 2013.02.19
+
{| 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"
| 5.0.1 || 2012.10.01
+
| 2.10 || 2013.02.26 || Current
|- class="ccn-table-even"
+
|}
| 5.0.0 || 2012.09.14
+
 
 +
 
 +
===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"
| 4.1.9 || 2011.12.01
+
| 2013.06.06 || 2014.03.06 ||
 
|- class="ccn-table-even"
 
|- class="ccn-table-even"
| 4.1.8 || circa 2011.06
+
| 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"
| 4.1.7 || circa 2011.11
+
| 13.1.1b || 2014.01.29 || Current
 
|- class="ccn-table-even"
 
|- class="ccn-table-even"
| 4.1.4 || circa 2009
+
| 12.0.2.5b || 2013.11.14 ||  
 
|- class="ccn-table-odd"
 
|- class="ccn-table-odd"
| 4.1.3 || circa 2009
+
| 11.0.5.4b || 2013.11.14 ||  
 
|- class="ccn-table-even"
 
|- class="ccn-table-even"
| 4.1.1 || circa 2008
+
| 12.0.0.0b || 2012.12.10 ||  
 
|- class="ccn-table-odd"
 
|- class="ccn-table-odd"
| 4.1.0 || circa 2008
+
| 11.0.0.0b || 2012.02.21 ||  
 
|- class="ccn-table-even"
 
|- class="ccn-table-even"
| 4.0.4 || circa 2008
+
| 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 ||
 
|}
 
|}
  
===AFNI===
 
[http://afni.nimh.nih.gov/afni/ Official Webste]
 
*vAFNI_2011_12_21_1014
 
**Install Date: 2012.03
 
  
===Chronux===
+
===FSL===
[http://www.chronux.org Official Website]
+
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]
*v2.10
+
**Install Date: 2013.02.26
+
[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 ||
 +
|}
  
===EEGLAB===
 
[http://sccn.ucsd.edu/eeglab/ Official Website]
 
*v12.0.0.0b
 
**Instal Date: 2012.12.10
 
*v11.0.0.0b
 
**Install Date: 2012.02.21
 
*v10.2.5.8b
 
**Install Date: 2012.02.21
 
  
===Caret===
 
[http://brainvis.wustl.edu/wiki/index.php/Caret:About Official Website]
 
*v5.65 2012.01.27
 
**Install Date: 2013.07.15
 
***Not folded into main profile yet.
 
  
 
===GCC===
 
===GCC===

Revision as of 20:40, 6 March 2014

Back to all things Hoffman2

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

Official Webste

Version Install Date Notes
2011_12_21_1014 circa 2012.03 Current


BrainSuite

Official Website

Version Number Install Date Notes
13a4 2014.03.05 Current


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


FreeSurfer

Official Website

Release Notes

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

Official Website

Revision History

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.
http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/
pydicom
pygments
PyMF
Python Matrix Factorization Module. Failed its tests though.
http://pymf.googlecode.com
pypr
PyQt4
pytz
pywt
pyximport
scikits
scipy
sklearn
sparsesvd
Singular Value Decomposition. Passed both tests.
http://pypi.python.org/pypi/sparsesvd
sphinx
sympy
traits
virtualenv
xcbgen