I tried to extract the thickness/volume value of the ROI labels transferred from the annot files that're generated automatically by FreeSurfer after a succesful group analysis with corrected significant results. However, the thickness/volume values are no longer correlated with the independent variable that I used in the group analysis model earlier and even the direction of group difference seems to be inconsistent with the group analysis results as well. I have no idea how it went wrong and wondered maybe there's something wrong with my scripts. Have any of you run into such kind of problem?
#annot2label:
mri_annotation2label --subject fsaverage --annotation onsetage_thickness --hemi rh --labelbase /expdata/wangyunxin/reconall_lj/fsaverage/labels/onsetage_thickness
for i in sub*
do
#label2label:
mri_label2label --srclabel fsaverage/labels/onsetage_thickness-001.label --srcsubject fsaverage --trglabel ./$i/labels/onsetage_thickness-001.label --trgsubject $i --regmethod surface --hemi rh
#label2stats:
mris_anatomical_stats -l $i/labels/onsetage_thickness-001.label -t $i/surf/rh.thickness -f $i/stats/rh.onsetage_thickness-001.stats -nsmooth 10 $i rh
done
#stats2table
aparcstats2table --subjectsfile /expdata/wangyunxin/reconall_lj/music/sublist48 --hemi rh --meas thickness --parc onsetage_thickness-001 --tablefile music/onsetage_thickness-001_rh.txt
Any suggestion would be great!
Thanks!
Best,
Yunxin