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Freesurfer

module avail freesurfer/

Freesurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data.

Usage

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).

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