Difference between revisions of "Freesurfer"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) |
||
| Line 10: | Line 10: | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
| Line 40: | Line 40: | ||
* FSFAST_HOME | * FSFAST_HOME | ||
* MNI_DIR | * MNI_DIR | ||
| − | |||
| − | |||
===Matlab configuration=== | ===Matlab configuration=== | ||
If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file: | If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file: | ||
| Line 47: | Line 45: | ||
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); | fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); | ||
path(path,fsfasttoolbox); | path(path,fsfasttoolbox); | ||
| + | or load the ''freesurfer'' module and run | ||
| + | source $HPC_FREESURFER_DIR/SetUpFreeSurfer.sh | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 73: | Line 73: | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | 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--> | <!--Installation--> | ||
Revision as of 22:21, 22 April 2013
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_{{#uppercase:freesurfer}}_DIR and FREESURFER_HOME - installation directory
- HPC_FREESURFER_BIN - executable directory
Freesurfer configuration variables
The following variables are preset by the freesurfer module:
- SUBJECTS_DIR
- FUNCTIONALS_DIR
- FSFAST_HOME
- MNI_DIR
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);
or load the freesurfer module and run
source $HPC_FREESURFER_DIR/SetUpFreeSurfer.sh
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.