Difference between revisions of "Hoffman2:Software Tools"

From Center for Cognitive Neuroscience
Jump to: navigation, search
m (16 revisions)
(Updating versions listed and changing to table layout.)
Line 10: Line 10:
 
===FSL===
 
===FSL===
 
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]
 
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]
*v5.0.4
+
**Install Date: 2013.06.18
+
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Revision History]
*v5.0.2
+
{| class="wikitable"
**Install Date: 2013.02.19
+
! class="ccn-table-header"| Version Number
*v5.0.1
+
! class="ccn-table-header"| Install Date
**Install Date: 2012.10.01
+
|- class="ccn-table-odd"
*v5.0.0
+
| 5.0.6 || 2013.12.18
**Install Date: 2012.09.14
+
|- class="ccn-table-even"
*v4.1.9
+
| 5.0.5 || 2013.10.17
**Install Date: 2011.12.01
+
|-class="ccn-table-odd"
*v4.1.8
+
| 5.0.4 || 2013.06.18
**Install Date: circa 2011.06
+
|- class="ccn-table-even"
*v4.1.7
+
| 5.0.2 || 2013.02.19
**Install Date: circa 2011.11
+
|- class="ccn-table-odd"
*v4.1.4
+
| 5.0.1 || 2012.10.01
**Install Date: circa 2009
+
|- class="ccn-table-even"
*v4.1.3
+
| 5.0.0 || 2012.09.14
**Install Date: circa 2009
+
|- class="ccn-table-odd"
*v4.1..1
+
| 4.1.9 || 2011.12.01
**Install Date: circa 2008
+
|- class="ccn-table-even"
*v4.1.0
+
| 4.1.8 || circa 2011.06
**Install Date: circa 2008
+
|- class="ccn-table-odd"
*v4.0.4
+
| 4.1.7 || circa 2011.11
**Install Date: circa 2008
+
|- 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
 +
|}
  
 
===FreeSurfer===
 
===FreeSurfer===
 
[http://surfer.nmr.mgh.harvard.edu/ Official Website]
 
[http://surfer.nmr.mgh.harvard.edu/ Official Website]
*v5.3.0
+
**Install Date: 2013.06.18
+
[http://freesurfer.net/fswiki/ReleaseNotes Release Notes]
*v5.2.0
+
 
**Install Date: 2013.03.27
+
{| class="wikitable"
*v5.1.0
+
! class="ccn-table-header" | Version
**Install Date: 2011.11.14
+
! class="ccn-table-header" | Install Date
*v5.0.0
+
|- class="ccn-table-odd"
**Install Date: circa 2010
+
| 5.3.0 || 2013.06.18
*v4.4.0
+
|- class="ccn-table-even"
**Install Date: circa 2009
+
| 5.2.0 || 2013.03.27
*v4.0.5
+
|- class="ccn-table-odd"
**Install Date: circa 2008
+
| 5.1.0 || 2011.11.14
 +
|- class="ccn-table-even"
 +
| 5.0.0 || circa 2010
 +
|- class="ccn-table-odd"
 +
| 4.4.0 || circa 2009
 +
|- class="ccn-table-even"
 +
| 4.0.5 || circa 2008
 +
|}
  
 
===AFNI===
 
===AFNI===

Revision as of 19:58, 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...

FSL

Official Website

Revision History

Version Number Install Date
5.0.6 2013.12.18
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

FreeSurfer

Official Website

Release Notes

Version Install Date
5.3.0 2013.06.18
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

AFNI

Official Webste

  • vAFNI_2011_12_21_1014
    • Install Date: 2012.03

Chronux

Official Website

  • v2.10
    • Install Date: 2013.02.26

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

Official Website

  • v5.65 2012.01.27
    • Install Date: 2013.07.15
      • Not folded into main profile yet.

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