Hoffman2:Software Tools: Difference between revisions
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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 | Below is a list of the available software tools. We will do our best to update it as changes are made. | ||
==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== | |||
[http://brainsuite.org/ Official Website] | [http://brainsuite.org/ Official Website] | ||
{| class="wikitable" | {| class="wikitable" | ||
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==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== | |||
[http://www.chronux.org Official Website] | [http://www.chronux.org Official Website] | ||
{| class="wikitable" | {| class="wikitable" | ||
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==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== | |||
[http://sccn.ucsd.edu/eeglab/ Official Website] | [http://sccn.ucsd.edu/eeglab/ Official Website] | ||
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==FreeSurfer== | |||
[http://surfer.nmr.mgh.harvard.edu/ Official Website] | [http://surfer.nmr.mgh.harvard.edu/ Official Website] | ||
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==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== | |||
[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== | |||
[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== | |||
[http://trackvis.org/ Official Website 1] | [http://trackvis.org/ Official Website 1] | ||
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==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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==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 | :Non-negative Matrix Factorization | ||
: | : | ||
:[http://nimfa.biolab.si/ http://nimfa.biolab.si/] | :[http://nimfa.biolab.si/ http://nimfa.biolab.si/] | ||
===nipype=== | |||
===nose=== | |||
===numpy=== | |||
===(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=== | |||
===pygments=== | |||
===PyMF=== | |||
: | :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=== | |||
===PyQt4=== | |||
===pytz=== | |||
===pywt=== | |||
===pyximport=== | |||
===scikits=== | |||
===scipy=== | |||
===sklearn=== | |||
===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=== | ||
===== | ===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. | |||
[http://mloss.org/software/view/48/] |
Revision as of 04:26, 3 October 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 as changes are made.
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 |
---|---|---|
5.0.7 | 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
Version Number | Install Date | Notes |
---|---|---|
080803 | 2009.11.19 | Current |
080128 | 2009.11.13 |
SPM
Version | Last Patch Applied | Last Checked Date | Notes |
---|---|---|---|
SPM8 | 5236 | 2014.01 | Current |
SPM5 | Unknown | N/A | No longer supported |
TrackVis/Diffusion Toolkit
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
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.
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.
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]