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
>
>
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>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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