Difference between revisions of "Freesurfer"

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[[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]][[Category:Neuroimaging]]
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[[Category:Software]][[Category:Bioinformatics]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|freesurfer}}
 
|{{#vardefine:app|freesurfer}}
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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.<!--Modules-->
 
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.<!--Modules-->
==Required Modules==
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==Environment Modules==
===Serial===
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_FREESURFER_BIN - executable directory
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===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==
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<!--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.
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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.
  
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.
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launch_freesurfer dcmunpack
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:
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'''NOTE:'''
  
$ module load freesurfer
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Freesurfer comes with Freeview software. Freeview is a completely separate software from Freesurfer and is used purely for data visualization. Freesurfer 6 includes Freeview 2.0.
$ 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-->

Latest revision as of 20:44, 10 June 2022

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.

Environment Modules

Run module spider freesurfer to find out what environment modules are available for this application.

System Variables

  • HPC_FREESURFER_DIR - 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

NOTE:

Freesurfer comes with Freeview software. Freeview is a completely separate software from Freesurfer and is used purely for data visualization. Freesurfer 6 includes Freeview 2.0.



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.