Difference between revisions of "Hoffman2:Software Tools"

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(Added in some more tools.)
(Updating FSL and Python/Gentoo tool information)
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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 [[Hoffman2:Profile|properly]].
 
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 [[Hoffman2:Profile|properly]].
  
Below is a list of the available software tools.  We will do our best to update it in real-time.
+
Below is a list of the available software tools.  We will do our best to update it as changes are made.
  
  
==List of Tools==
+
==AFNI==
Under Construction...
 
 
 
 
 
===AFNI===
 
 
[http://afni.nimh.nih.gov/afni/ Official Webste]
 
[http://afni.nimh.nih.gov/afni/ Official Webste]
 
{| class="wikitable"
 
{| class="wikitable"
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===BrainSuite===
+
==BrainSuite==
 
[http://brainsuite.org/ Official Website]
 
[http://brainsuite.org/ Official Website]
 
{| class="wikitable"  
 
{| class="wikitable"  
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===Caret===
+
==Caret==
 
[http://brainvis.wustl.edu/wiki/index.php/Caret:About Official Website]
 
[http://brainvis.wustl.edu/wiki/index.php/Caret:About Official Website]
 
{| class="wikitable"
 
{| class="wikitable"
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===Chronux===
+
==Chronux==
 
[http://www.chronux.org Official Website]
 
[http://www.chronux.org Official Website]
 
{| class="wikitable"
 
{| class="wikitable"
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===dcm2nii===
+
==dcm2nii==
 
[http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html Official Website]
 
[http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html Official Website]
 
{| class="wikitable"
 
{| class="wikitable"
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===EEGLAB===
+
==EEGLAB==
 
[http://sccn.ucsd.edu/eeglab/ Official Website]
 
[http://sccn.ucsd.edu/eeglab/ Official Website]
 
   
 
   
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===FreeSurfer===
+
==FreeSurfer==
 
[http://surfer.nmr.mgh.harvard.edu/ Official Website]
 
[http://surfer.nmr.mgh.harvard.edu/ Official Website]
 
   
 
   
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===FSL===
+
==FSL==
 
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]
 
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]
 
   
 
   
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! 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-even"
 +
| 5.0.7 || 2013.10.17 ||
 
|- class="ccn-table-odd"
 
|- class="ccn-table-odd"
| 5.0.6 || 2013.12.18 || Current
+
| 5.0.6 || 2013.12.18 || Current (2013.12.18-)
 
|- class="ccn-table-even"
 
|- class="ccn-table-even"
| 5.0.5 || 2013.10.17 ||
+
| 5.0.5 || 2013.10.17 || (2013.10.17-2013.12.17)
 
|-class="ccn-table-odd"
 
|-class="ccn-table-odd"
 
| 5.0.4 || 2013.06.18 ||
 
| 5.0.4 || 2013.06.18 ||
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===ITKGray===
+
==ITKGray==
 
[http://vistalab.stanford.edu/newlm/index.php/ItkGray Official Website]
 
[http://vistalab.stanford.edu/newlm/index.php/ItkGray Official Website]
 
{| class="wikitable"  
 
{| class="wikitable"  
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===SPM===
+
==SPM==
 
[http://www.fil.ion.ucl.ac.uk/spm/ Official Website]
 
[http://www.fil.ion.ucl.ac.uk/spm/ Official Website]
 
{| class="wikitable"
 
{| class="wikitable"
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===TrackVis/Diffusion Toolkit===
+
==TrackVis/Diffusion Toolkit==
 
[http://trackvis.org/ Official Website 1]
 
[http://trackvis.org/ Official Website 1]
 
   
 
   
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===WEKA===
+
==WEKA==
 
[http://www.cs.waikato.ac.nz/ml/weka/ Official Website]
 
[http://www.cs.waikato.ac.nz/ml/weka/ Official Website]
 
{| class="wikitable"  
 
{| class="wikitable"  
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===GCC===
 
===LAPACK===
 
===BLAS===
 
===GLIB===
 
===C++===
 
===CMake===
 
===CPACK===
 
===MPI Kmeans===
 
See this website for how to cite using the MPI Kmeans tool.
 
[http://mloss.org/software/view/48/]
 
  
===Python2.7===
+
==Python2.7==
====Packages====
+
Gentoo Prefix version of Python 2.7.  Site packages listed below were installed using pip unless otherwise noted.
=====CVXOPT=====
+
Installed by pip unless otherwise noted
=====Cython=====
+
===CVXOPT===
=====Gnuplot=====
+
===Cython===
=====IPython=====
+
===Gnuplot===
=====matplotlib=====
+
===IPython===
=====nibabel=====
+
===matplotlib===
=====nifti=====
+
:Installed by Gentoo prefix
=====nimfa=====
+
===nibabel===
 +
===nifti===
 +
===nimfa===
 
:Non-negative Matrix Factorization
 
:Non-negative Matrix Factorization
 
:
 
:
 
:[http://nimfa.biolab.si/ http://nimfa.biolab.si/]
 
:[http://nimfa.biolab.si/ http://nimfa.biolab.si/]
=====nipype=====
+
===nipype===
=====nose=====
+
===nose===
=====numpy=====
+
===numpy===
=====(p)lsa=====
+
===(p)lsa===
 
:(probabilistic) Latent Semantic Analysis.  Failed its tests.py though.
 
:(probabilistic) Latent Semantic Analysis.  Failed its tests.py though.
  
 
:[http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/ http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/]
 
:[http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/ http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/]
=====pydicom=====
+
===pydicom===
=====pygments=====
+
===pygments===
=====PyMF=====
+
===PyMF===
:Python Matrix Factorization Module.  Failed its tests though.
+
:python Matrix Factorization Module.  Failed its tests though.
  
 
:[http://pymf.googlecode.com http://pymf.googlecode.com]
 
:[http://pymf.googlecode.com http://pymf.googlecode.com]
=====pypr=====
+
===pypr===
=====PyQt4=====
+
===PyQt4===
=====pytz=====
+
===pytz===
=====pywt=====
+
===pywt===
=====pyximport=====
+
===pyximport===
=====scikits=====
+
===scikits===
=====scipy=====
+
===scipy===
=====sklearn=====
+
===sklearn===
=====sparsesvd=====
+
===sparsesvd===
 
:Singular Value Decomposition.  Passed both tests.
 
:Singular Value Decomposition.  Passed both tests.
  
 
:[http://pypi.python.org/pypi/sparsesvd http://pypi.python.org/pypi/sparsesvd]
 
:[http://pypi.python.org/pypi/sparsesvd http://pypi.python.org/pypi/sparsesvd]
=====sphinx=====
+
===sphinx===
=====sympy=====
+
===sympy===
=====traits=====
+
===traits===
=====virtualenv=====
+
===virtualenv===
=====xcbgen=====
+
===xcbgen===
 +
 
 +
 
 +
==GCC==
 +
==LAPACK==
 +
==BLAS==
 +
==GLIB==
 +
==C++==
 +
==CMake==
 +
==CPACK==
 +
==MPI Kmeans==
 +
See this website for how to cite using the MPI Kmeans tool.
 +
[http://mloss.org/software/view/48/]

Revision as of 04:26, 3 October 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 as changes are made.


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
5.0.7 2013.10.17
5.0.6 2013.12.18 Current (2013.12.18-)
5.0.5 2013.10.17 (2013.10.17-2013.12.17)
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


ITKGray

Official Website

Version Number Install Date Notes
080803 2009.11.19 Current
080128 2009.11.13


SPM

Official Website

Version Last Patch Applied Last Checked Date Notes
SPM8 5236 2014.01 Current
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 Number Install Date Notes
3.7.10 2014.03.03 Current
3.6.5 circa 2011.08


Python2.7

Gentoo Prefix version of Python 2.7. Site packages listed below were installed using pip unless otherwise noted. Installed by pip unless otherwise noted

CVXOPT

Cython

Gnuplot

IPython

matplotlib

Installed by Gentoo prefix

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

GCC

LAPACK

BLAS

GLIB

C++

CMake

CPACK

MPI Kmeans

See this website for how to cite using the MPI Kmeans tool. [1]