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Group Analysis (baseline)
- Sophie Matis
FreeSurfer group analysis can either be carried out with the graphical interface, Qdec, or by creating your own GLM and contrasts and running mri_glmfit on the command line. Instructions for both these methods can be found on the FreeSurfer wiki pages linked above. In both cases you will need to smooth the data first. This can be done with the following script on Artemis.
Before running the script you will need to add in the project name, SUBJECTS_DIR, and a subject list.
#PBS -P
#PBS -N QDECproc
#PBS -l select=1:ncpus=2:mem=32GB
#PBS -l walltime=10:00:00
#PBS -q defaultQ
module load mrtrix3/3.0.1
module load freesurfer/6.0.0
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/scratch/Project/Folder
cd $SUBJECTS_DIR
sub_list='FTDXXXX
FTDXXXX
FTDXXXX
'
cp -r /usr/local/freesurfer/6.0.0/subjects/fsaverage ${SUBJECTS_DIR}
for i in $sub_list ; do
mv ${SUBJECTS_DIR}/${i}/${i}_FreeSurferAnat/* ${SUBJECTS_DIR}/${i}/;
mris_preproc --s ${i} --hemi lh --meas thickness --fwhm 15 --target fsaverage --out ${i}/surf/lh.thickness.fwhm15.fsaverage.mgh;
mris_preproc --s ${i} --hemi rh --meas thickness --fwhm 15 --target fsaverage --out ${i}/surf/rh.thickness.fwhm15.fsaverage.mgh;
mris_preproc --s ${i} --hemi lh --meas thickness --fwhm 20 --target fsaverage --out ${i}/surf/lh.thickness.fwhm20.fsaverage.mgh;
mris_preproc --s ${i} --hemi rh --meas thickness --fwhm 20 --target fsaverage --out ${i}/surf/rh.thickness.fwhm20.fsaverage.mgh;
done
After carrying out statistical analysis with QDEC or the glmfit command, you can correct the results for multiple comparisons using the below code. Please refer to the link for descriptions of each option, how to change the vertex-wise and cluster-wise thresholds, and how to do a one-sided test.
#PBS -P
#PBS -N FScorrection
#PBS -l select=1:ncpus=4:mem=32GB
#PBS -l walltime=2:00:00
#PBS -q defaultQ
module load freesurfer/6.0.0
source $FREESURFER_HOME/SetUpFreeSurfer.sh
##Add the subject directory location and the location of all the glm directories below##
export SUBJECTS_DIR=
glmdir=/scratch/long_fixel_FTD/CorticalThickness/Data/qdec/
cd $SUBJECTS_DIR
list=$(ls ${glmdir})
for i in $list_ ; do
mri_glmfit-sim \
--glmdir ${glmdir}${i} \
--perm 1000 3.0 abs \
--cwp 0.05 \
--2spaces \
--bg 4 ;
done