Difference between revisions of "Freesurfer"
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− | [[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]] | + | [[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]][[Category:Neuroimaging]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|freesurfer}} | |{{#vardefine:app|freesurfer}} | ||
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
− | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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--> | --> | ||
==System Variables== | ==System Variables== | ||
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory |
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<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#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. | |
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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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|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> |
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.