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 account properly.
Setting Up Your Account to Access the Tools
- NOTE: If you've never used a *NIX text editor, please read a bit about some of them here before proceeding.
In order to access all the great software packages that have been installed on Hoffman2 for the FMRI usergroup (list below), you need to edit your Bash Profile on the cluster. Follow these easy steps:
- SSH into Hoffman2 and make sure you are in your home directory (type the command
cd
and press enter). - Open the file .bash_profile for editing. With VIM you would type
- Paste in the lines
source /u/home/FMRI/apps/etc/profile umask 007
- Save and close out the file
- Log out of Hoffman2. The next time you log in, extra login messages will appear and you will have access to the FMRI usergroup software packages.
List of Tools
Under Construction...
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.