@Ziqian-Wang and I want to use mrcentre to obtain coordinates of rois as input for the -line argument of the tckresample command.
We have two roi files and a problem with our roi_pons.mif file.
When we calculate the center of mass using mrcentre in the scanner coordinate system we get a position somewhere in the cerebellum, outside of the roi.
‘Preprocessing’ the roi file using mrcrop with the same input image as a mask
mrcrop roi_pons.mif roi_pons_cropped.mif -mask roi_pons.mif
and using the cropped output with mrcentre gives correct coordinates.
Do you have an idea why there’s this difference in the mrcentre results? Do zero-valued voxels have an effect on the resulft of mrcentre?