Difference between revisions of "Freesurfer"

From UFRC
Jump to navigation Jump to search
Line 33: Line 33:
 
==System Variables==
 
==System Variables==
 
* HPC_{{#uppercase:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory
 
* HPC_{{#uppercase:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory
* HPC_FREESURFER_BIN - executable directory
+
 
===Freesurfer configuration variables===
 
The following variables are preset by the {{#var:app}} module:
 
* SUBJECTS_DIR
 
* FUNCTIONALS_DIR
 
* FSFAST_HOME
 
* MNI_DIR
 
===Matlab configuration===
 
If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file:
 
fsfasthome = getenv('FSFAST_HOME');
 
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
 
path(path,fsfasttoolbox);
 
or load the ''freesurfer'' module and run
 
source $HPC_FREESURFER_DIR/SetUpFreeSurfer.sh
 
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 53: Line 40:
 
<!--Run-->
 
<!--Run-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
If you encounter a NVIDIA video driver compatibility issue with FreeView try the following workaround.
+
Starting with freesurfer/6.0.0 the software is available as a Singularity container. To run any executable use the 'launch_freesurfer' wrapper after loading the module.
  
The freeview program uses OpenGL extensions, which appear to be driver-dependent. If you're running freeview on gui.rc.ufl.edu or gui1.rc.ufl.edu you can get freeview to run within an 'xpra' session, which will handle GLX automatically.
+
E.g.
1. Install Xpra on your client machine - see (https://www.xpra.org)
 
2. Log into gui or gui1 node and start freeview as follows:pick a random PORT number from 1000 to 50000
 
  
For example, for user USERNAME, GUI node gui1.rc.ufl.edu, and port 3223 we can do the following:
+
launch_freesurfer dcmunpack
  
$ module load freesurfer
 
$ module unload python
 
$ xpra start :PORT --start-child=freeview
 
in this case
 
$ xpra start :3223 --start-child=freeview
 
Attach to the xpra session from your local machine with
 
$ xpra attach ssh:USERNAME@gui1.rc.ufl.edu:3223
 
  
A freeview window should show up on your local desktop.
 
 
|}}
 
|}}
 
<!--PBS scripts-->
 
<!--PBS scripts-->

Revision as of 12:56, 31 March 2017

Description

freesurfer website  

Freesurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

Required Modules

Serial

  • freesurfer

System Variables

  • HPC_{{#uppercase:freesurfer}}_DIR and FREESURFER_HOME - installation directory


Additional Information

Starting with freesurfer/6.0.0 the software is available as a Singularity container. To run any executable use the 'launch_freesurfer' wrapper after loading the module.

E.g.

launch_freesurfer dcmunpack



Citation

If you publish research that uses freesurfer you have to cite it as follows:

See [1] in the Freesurfer wiki on how to correctly cite Freesurfer tools.