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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.


Freely available for every user. Modules:



Licence of The General Hospital Corporation, Boston MA:


Initialize module with command:

module add freesurfer-5.3.0

After initialization are available all required system variables and program binaries. Variable are easily changeable through shell.

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

Program manager