Difference between revisions of "Freesurfer"

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[[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]]
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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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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
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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==
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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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.
 +
 
 +
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.
 +
 
 
|}}
 
|}}
 
<!--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.