Biowulf High Performance Computing at the NIH
Pysurfer on Biowulf

Pysurfer is a python package for visualization of brain surfaces and functional activity obtained from neuroimaging datasets

Web site

Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Pysurfer is meant to be used interactively. Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pysurfer

[user@cn3144 ~]$ ipython

In [1]: from surfer import Brain
In [2]: %gui qt
In [3]: dir='/data/myusername/PYSURFER-EXAMPLES/tutorial_data/buckner_data/tutorial_subjs/'
In [4]: subject_id = 'fsaverage'
In [5]: hemi = 'lh'
In [6]: surface = 'inflated'
In [7]: brain = Brain(subject_id, hemi, surface, subjects_dir=dir)
In [8]: exit

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$