Hoffman2:Software Tools

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Revision as of 21:24, 6 March 2014 by Elau (talk | contribs) (Added in some more tools.)

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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


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


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