Difference between revisions of "Freesurfer"
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− | == | + | [[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]][[Category:Neuroimaging]] |
− | + | {|<!--CONFIGURATION: REQUIRED--> | |
+ | |{{#vardefine:app|freesurfer}} | ||
+ | |{{#vardefine:url|http://surfer.nmr.mgh.harvard.edu/}} | ||
+ | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
+ | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
+ | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> | ||
+ | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
+ | |{{#vardefine:policy|}} <!--POLICY--> | ||
+ | |{{#vardefine:testing|}} <!--PROFILING--> | ||
+ | |{{#vardefine:faq|}} <!--FAQ--> | ||
+ | |{{#vardefine:citation|1}} <!--CITATION--> | ||
+ | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
+ | |} | ||
+ | <!--BODY--> | ||
+ | <!--Description--> | ||
+ | {{#if: {{#var: url}}| | ||
+ | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
− | + | 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== |
− | + | ===Serial=== | |
− | + | * {{#var:app}} | |
− | + | <!-- | |
− | + | ===Parallel (OpenMP)=== | |
− | + | * intel | |
− | + | * {{#var:app}} | |
− | + | ===Parallel (MPI)=== | |
− | + | * intel | |
+ | * openmpi | ||
+ | * {{#var:app}} | ||
+ | --> | ||
+ | ==System Variables== | ||
+ | * HPC_{{uc:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory | ||
− | + | <!--Configuration--> | |
+ | {{#if: {{#var: conf}}|==Configuration== | ||
+ | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details. | ||
+ | |}} | ||
+ | <!--Run--> | ||
+ | {{#if: {{#var: exe}}|==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. | |
− | + | |}} | |
+ | <!--PBS scripts--> | ||
+ | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
+ | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples. | ||
+ | |}} | ||
+ | <!--Policy--> | ||
+ | {{#if: {{#var: policy}}|==Usage Policy== | ||
+ | WRITE USAGE POLICY HERE (Licensing, usage, access). | ||
+ | |}} | ||
+ | <!--Performance--> | ||
+ | {{#if: {{#var: testing}}|==Performance== | ||
+ | WRITE_PERFORMANCE_TESTING_RESULTS_HERE | ||
+ | |}} | ||
+ | <!--Faq--> | ||
+ | {{#if: {{#var: faq}}|==FAQ== | ||
+ | *'''Q:''' **'''A:'''|}} | ||
+ | <!--Citation--> | ||
+ | {{#if: {{#var: citation}}|==Citation== | ||
+ | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
− | + | See [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation] in the Freesurfer wiki on how to correctly cite Freesurfer tools. | |
− | + | |}} | |
− | + | <!--Installation--> | |
− | + | {{#if: {{#var: installation}}|==Installation== | |
− | + | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | |
− | + | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | |
− | + | __NOTOC____NOEDITSECTION__ | |
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Revision as of 21:20, 6 December 2019
Description
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.