Hoffman2:Software Tools: Difference between revisions
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==Caret== | ==Caret== | ||
Revision as of 18:45, 6 March 2017
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 |
|---|---|---|
| 2016.10.18-16.3.11 | 2016.11.20 | Current |
BrainSuite
| Version Number | Install Date | Notes |
|---|---|---|
| 15c | 2016.02.18 | 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 | Current (2014.10.10-) |
| 5.0.6 | 2013.12.18 | (2013.12.18-2014.10.10) |
| 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]