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...) |
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| − | == | + | [[Category:Software]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]] |
| − | + | {|<!--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--> | |
| − | < | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | < | + | ==System Variables== |
| − | + | * HPC_{{uc:{{#var:app}}}}_DIR - 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__ | ||
Latest revision as of 20:09, 12 August 2022
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.
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.