Hoffman2:Software Tools

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 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:

1. SSH into Hoffman2 and make sure you are in your home directory (type the command cd and press enter).
2. Open the file .bash_profile for editing. With VIM you would type

   With VIM you would type

   $ vim .bash_profile

   With Emacs you would type

   $ emacs .bash_profile

3. Paste in the lines

   source /u/home/FMRI/apps/etc/profile

   umask 007

4. Save and close out the file

   With VIM you would type

   ESC + ":wq" + ENTER

   With Emacs you would type

   CTRL+x, CTRL+c

5. Logout 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...

MPI Kmeans

See this website for how to cite using the MPI Kmeans tool. [1]

Python2.7

Packages

nimfa

Non-negative Matrix Factorization

http://nimfa.biolab.si/

(p)lsa

(probabilistic) Latent Semantic Analysis. Failed its tests.py though.

http://www.mblondel.org/journal/2010/06/13/lsa-and-plsa-in-python/

PyMF

Python Matrix Factorization Module. Failed its tests though.

http://pymf.googlecode.com

sparsesvd

Singular Value Decomposition. Passed both tests.

http://pypi.python.org/pypi/sparsesvd