Hoffman2:Software Tools
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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 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
- v5.0.4
- Install Date: 2013.06.18
- v5.0.2
- Install Date: 2013.02.19
- v5.0.1
- Install Date: 2012.10.01
- v5.0.0
- Install Date: 2012.09.14
- v4.1.9
- Install Date: 2011.12.01
- v4.1.8
- Install Date: circa 2011.06
- v4.1.7
- Install Date: circa 2011.11
- v4.1.4
- Install Date: circa 2009
- v4.1.3
- Install Date: circa 2009
- v4.1..1
- Install Date: circa 2008
- v4.1.0
- Install Date: circa 2008
- v4.0.4
- Install Date: circa 2008
FreeSurfer
- v5.3.0
- Install Date: 2013.06.18
- v5.2.0
- Install Date: 2013.03.27
- v5.1.0
- Install Date: 2011.11.14
- v5.0.0
- Install Date: circa 2010
- v4.4.0
- Install Date: circa 2009
- v4.0.5
- Install Date: circa 2008
AFNI
- vAFNI_2011_12_21_1014
- Install Date: 2012.03
Chronux
- v2.10
- Install Date: 2013.02.26
EEGLAB
- 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
- v5.65 2012.01.27
- Install Date: 2013.07.15
- Not folded into main profile yet.
- Install Date: 2013.07.15
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.
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.