Difference between revisions of "Freesurfer"

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.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]]
+[[Category:Software]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|freesurfer}}
@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
 |{{#vardefine:testing|}}       <!--PROFILING-->
 |{{#vardefine:faq|}}             <!--FAQ-->
-|{{#vardefine:citation|}}       <!--CITATION-->
+|{{#vardefine:citation|1}}       <!--CITATION-->
 |{{#vardefine:installation|}} <!--INSTALLATION-->
 |}
@@ Line 19: / Line 19: @@
 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==
+==Environment Modules==
-===Serial===
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR and FREESURFER_HOME - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* HPC_FREESURFER_BIN - executable directory
-===Freesurfer configuration variables===
-The following variables are preset by the {{#var:app}} 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);
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 53: / Line 30: @@
 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+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-->
@@ Line 73: / Line 59: @@
 {{#if: {{#var: citation}}|==Citation==
 If you publish research that uses {{#var:app}} you have to cite it as follows:
-WRITE_CITATION_HERE
+See [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation] in the Freesurfer wiki on how to correctly cite Freesurfer tools.
 |}}
 <!--Installation-->