Difference between revisions of "Freesurfer"

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==Environment Variables==
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[[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]][[Category:Neuroimaging]]
In order for Freesurfer to work, the followings environment variables need to be set:
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{|<!--CONFIGURATION: REQUIRED-->
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|{{#vardefine:app|freesurfer}}
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|{{#vardefine:url|http://surfer.nmr.mgh.harvard.edu/}}
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
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|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
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|{{#vardefine:policy|}}        <!--POLICY-->
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|{{#vardefine:testing|}}      <!--PROFILING-->
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|{{#vardefine:faq|}}            <!--FAQ-->
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|{{#vardefine:citation|1}}      <!--CITATION-->
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|{{#vardefine:installation|}} <!--INSTALLATION-->
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|}
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<!--BODY-->
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<!--Description-->
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{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
In bash:
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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-->
<pre>
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==Required Modules==
$ export FREESURFER_HOME=/apps/freesurfer
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===Serial===
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
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* {{#var:app}}
</pre>
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<!--
In tcsh:
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===Parallel (OpenMP)===
<pre>
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* intel
$ setenv FREESURFER_HOME /apps/freesurfer
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* {{#var:app}}
$ source $FREESURFER_HOME/SetUpFreeSurfer.csh
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===Parallel (MPI)===
</pre>
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* intel
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* openmpi
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* {{#var:app}}
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-->
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory
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<!--Configuration-->
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{{#if: {{#var: conf}}|==Configuration==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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|}}
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<!--Run-->
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{{#if: {{#var: exe}}|==Additional Information==
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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.
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E.g.
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launch_freesurfer dcmunpack
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'''NOTE:'''
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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.
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|}}
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<!--PBS scripts-->
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{{#if: {{#var: pbs}}|==PBS Script Examples==
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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|}}
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<!--Policy-->
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{{#if: {{#var: policy}}|==Usage Policy==
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WRITE USAGE POLICY HERE (Licensing, usage, access).
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|}}
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<!--Performance-->
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{{#if: {{#var: testing}}|==Performance==
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WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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|}}
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<!--Faq-->
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{{#if: {{#var: faq}}|==FAQ==
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*'''Q:''' **'''A:'''|}}
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<!--Citation-->
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{{#if: {{#var: citation}}|==Citation==
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If you publish research that uses {{#var:app}} you have to cite it as follows:
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See [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation] in the Freesurfer wiki on how to correctly cite Freesurfer tools.
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|}}
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<!--Installation-->
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{{#if: {{#var: installation}}|==Installation==
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
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__NOTOC____NOEDITSECTION__

Latest revision as of 21:20, 6 December 2019

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_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

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.