Difference between revisions of "Freesurfer"
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(New page: ==Environment Variables== In order for Freesurfer to work, the followings environment variables need to be set: In bash: <pre> $ export FREESURFER_HOME=/apps/freesurfer </pre> In tcsh: <p...) |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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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__ | ||
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.