Freesurfer

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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.

License

Licence of The General Hospital Corporation, Boston MA: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of freesurfer and load default version of freesurfer as

module avail freesurfer/ # list available modules
module load freesurfer   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail freesurfer

and choose explicit version you want to use.

Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.

Parallel usage

For parallel use you can run the job on the multiprocessor machine (with proper amount of memory) and add the proper switch to freesurfer tools which supports it. For example to the mri_glmfit-sim you can add --bg number_of_processors parameter. On the basis of tutorial and downloaded data set you can use following example:

qsub -X -I -q short -l nodes=1:ppn=8,mem=4gb#excl
...
export SUBJECTS_DIR=/scratch/hanousek/fsf_demo/samples/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/glm
mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir
mri_glmfit-sim --glmdir lh.gender_age.glmdir --sim mc-z 100 4 mc-z.negative --sim-sign neg --overwrite --bg 8

Computing of 100 iterations run by the last row lasts without 8-processor parallelization (without parameter --bg 8) approx. 50 minutes, with parallelization about 8 minutes. You can use more processors to shorten the computing.

Possible faults

Memory allocation

Memory allocation failure, ie:

reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
*** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x0000000029b768d0 ***

Occured while try the submission:

/storage/brno2/home/hanousek/inst/freesurfer_project/samples/buckner_data/tutorial_subjs/glm$ mri_glmfit-sim --glmdir lh.gender_age.glmdir --sim mc-z 40 4 mc-z.negative --sim-sign neg --overwrite

after adding the --bg 8 was everything OK.

Conclusion: Maybe it depends on the count of executed iterations defined by --sim mc-z 40 4 mc-z.negative parameter (here 40).

Documentation

Documentation and support are at wiki of Freesurfer project. Valuable tutorial i available at University of Texas.

Homepage

http://surfer.nmr.mgh.harvard.edu/