On 05/24/2017 03:30 PM, gaubert wrote:
Hello,
I am performing a group analysis to compare the cortical thickness between controls and patients (in fsaverage space with a smooth of 15) and I obtain two clusters. I want to extract the average cortical thickness in these clusters for each participant of the analysis. And I have a couple of questions on this extraction:
1/ when I take a look at the generated files during the processing, there is a file named "cache.th20.pos.y.ocn.dat" which contained (from FS wiki) "the average value of each subject in each cluster". Is that right that these values are generated from individuals "rh.thickness.fwhm15.fsaverage.mgh" files (meaning, they are in the fsaverage space with smooth at 15)?
Yes
2/ I try to perform this extraction in native space (without smooth). And I wanted to be sure that my process is correct. Here are the different steps:
1_ Get the labels from annotation files: mri_annotation2label--subject fsaverage --hemi $hemi --labelbase './'$annot_filename'_label' --annotation ${contrast_dir}/${annot_filename}.annot
2_ register the clusters to native space: mri_label2label --srclabel'./'$annot_filename'_label-001.label' --srcsubject fsaverage --trgsubject $subj --trglabel $trg_label --regmethod surface --hemi $hemi
3_ get thickness in the cluster: mris_anatomical_stats -l $trg_label-t ${SUBJECTS_DIR}'/'${subj}'/surf/'${hemi}'.thickness' -f $th_result_filename -b $subj $hemi
Yes, that is correct. Note that you will not get the same results as from the ocn.dat file
Thanks for your help.
Malo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer