Hoffman2:Software Tools: Difference between revisions

Revision as of 19:44, 25 April 2012

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...

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.

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

pypr

PyQt4

pytz

pywt

pyximport

scikits

scipy

sklearn

sparsesvd

Singular Value Decomposition. Passed both tests.

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

@@ Line 1: / Line 1: @@
 [[Hoffman2|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.
+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]].
-==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 [[Text Editors|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:
-# [[Hoffman2:Accessing the Cluster#SSH - Command Line|SSH into Hoffman2]] and make sure you are in your home directory (type the command <code>cd</code> and press enter).
-# Open the file '''.bash_profile''' for editing.  With [[Text Editors#Vim|VIM]] you would type
-#: With [[Text Editors#Vim|VIM]] you would type
-#:: <pre>$ vim .bash_profile</pre>
-#: With [[Text Editors#Emacs|Emacs]] you would type
-#:: <pre>$ emacs .bash_profile</pre>
-# Paste in the lines
-#:<pre>source /u/home/FMRI/apps/etc/profile&#10;umask 007</pre>
-# Save and close out the file
-#: With [[Text Editors#Vim|VIM]] you would type
-#:: <code>ESC + ":wq" + ENTER</code>
-#: With [[Text Editors#Emacs|Emacs]] you would type
-#:: <code>CTRL+x, CTRL+c</code>
-# 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.
+Below is a list of the available software tools.  We will do our best to update it in real-time.