Difference between revisions of "Freesurfer"

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==Description==
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[[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]]
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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.
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{|<!--CONFIGURATION: REQUIRED-->
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|{{#vardefine:app|freesurfer}}
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[http://surfer.nmr.mgh.harvard.edu/fswiki FreeSurfer Website]
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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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==Environment Variables==
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|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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In order for Freesurfer to work, the followings environment variables need to be set:
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|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
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In bash:
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|{{#vardefine:policy|}}        <!--POLICY-->
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<pre>
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|{{#vardefine:testing|}}      <!--PROFILING-->
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$ export FREESURFER_HOME=/apps/freesurfer
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|{{#vardefine:faq|}}            <!--FAQ-->
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$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
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|{{#vardefine:citation|}}      <!--CITATION-->
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</pre>
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|{{#vardefine:installation|}} <!--INSTALLATION-->
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In tcsh:
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|}
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<pre>
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<!--BODY-->
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$ setenv FREESURFER_HOME /apps/freesurfer
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<!--Description-->
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$ source $FREESURFER_HOME/SetUpFreeSurfer.csh
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{{#if: {{#var: url}}|
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</pre>
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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In fact, you are going to have to grab the SetUpFreeSurfer script and copy it to your home directory so that it can be modified, as we do not have space in the installation area of the software for you to copy your image files to.
 
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It is recommended that you copy your image files over to /scratch/hpc/$username and work on the files there, as that is where the fastest filesystem is located.
 
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==Optional Configuration Settings==
 
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The defaults declared in the SetUpFreeSurfer.csh script should work for most installations. However, users should feel free to edit this file to customize certain environment variables:
 
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1. Your declaration of the FREESURFER_HOME variable could be moved within the SetUpFreeSurfer.csh script.
 
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2. The default SUBJECTS_DIR, which is $FREESURFER_HOME/subjects, is most likely the first variable that you will want to customize, as you may keep different groups of subjects in different directories. You may include the following either directly in the SetUpFreeSurfer.csh script, or prior to calling it:
 
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      setenv SUBJECTS_DIR <full path to subject dir>  
 
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3. If you do NOT intend to use the functional tools, then add the following line to the additional configuration section:
 
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      setenv NO_FSFAST
 
  
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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-->
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==Required Modules==
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===Serial===
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* {{#var:app}}
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<!--
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===Parallel (OpenMP)===
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* intel
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* {{#var:app}}
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===Parallel (MPI)===
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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_{{#uppercase:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory
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* HPC_FREESURFER_BIN - executable directory
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===Freesurfer configuration variables===
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The following variables are preset by the {{#var:app}} module:
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* SUBJECTS_DIR
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* FUNCTIONALS_DIR
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* FSFAST_HOME
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* MNI_DIR
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or load the ''freesurfer'' module and run
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source $HPC_FREESURFER_DIR/SetUpFreeSurfer.sh
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===Matlab configuration===
 
If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file:
 
If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file:
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fsfasthome = getenv('FSFAST_HOME');
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      fsfasthome = getenv('FSFAST_HOME');
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fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
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      fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
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path(path,fsfasttoolbox);
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      path(path,fsfasttoolbox);
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<!--Configuration-->
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{{#if: {{#var: conf}}|==Configuration==
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4. You may also wish to declare a path to an FSL installation you might have:
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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|}}
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      setenv FSL_DIR /usr/local/fsl
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<!--Run-->
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{{#if: {{#var: exe}}|==Additional Information==
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5. Save the file. You will need to source this file (SetUpFreeSurfer.csh) every time you want to use Freesurfer.
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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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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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WRITE_CITATION_HERE
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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__

Revision as of 22:19, 22 April 2013

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
  • HPC_FREESURFER_BIN - executable directory

Freesurfer configuration variables

The following variables are preset by the freesurfer module:

  • SUBJECTS_DIR
  • FUNCTIONALS_DIR
  • FSFAST_HOME
  • MNI_DIR

or load the freesurfer module and run 

source $HPC_FREESURFER_DIR/SetUpFreeSurfer.sh

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);





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