I have been running into issues trying to obtain the centroid coordinates of an ROI that spans a large curved region. The center of mass is outside the ROI because of its shape. See attached for an example in volumetric space, the crosshairs point to the calculated centroid coordinate and the ROI is colored in yellow.
My approach has been to use
mri_surfcluster in freesurfer to obtain centroid coordinates in MNI from the cortical surface as follows:
mri_surfcluster --in $SUBJECTS_DIR/fsaverage6/surf/rh.curv \ --clabel $SUBJECTS_DIR/Schaefer2018_100Parcels_7Networks_order_fsaverage6_labels/rh.7Networks_RH_Default_PFCm_2.label \ --sum $SUBJECTS_DIR/Schaefer2018_100Parcels_7Networks_order_fsaverage6_labels/summary.txt \ --centroid \ --thmin 0.000001 \ --hemi rh \ --subject fsaverage6 \ --nofixmni
The reason why I am deriving centroid coordinates from the cortical surface is because the ROI was originally derived on the cortical surface.
I have also tried deriving centroid coordinates after transforming the ROI into volumetric space. I used
fslstats on the volume with the
-C flag to obtain the coordinates. I pretty much receive the same results where the centroid is outside the ROI.
The ROI has been obtained from Schaefer et al. 2018 Cerebral Cortex 100 area parcellation (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal).
Any advice or suggestions would be helpful, thank you!