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

Web site

• Home page

• Pysurfer Documentation

• Module Name: pysurfer (see the modules page for more information)

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 ~]$