Hi Freesurfer team,
I have a compressed nifti file converted from DICOM that I am running through recon-all. From my understanding first mri_convert is run on the original nifti file in order to generate 001.mgz which is then averaged across multiple runs to make rawavg.mgz. Since I'm only using 1 run, rawavg.mgz should be equivalent to 001.mgz. Now I've noticed that compared to simply loading in the original NIFTI image, loading in rawavg.mgz produces a cropped version of the image where the bottom section (neck region and below) is cropped out. In addition the SI axis which used to be 255 voxels in height, is now shorter (different across individuals run through recon-all). With a set of voxel indices in the original NIFTI image, I'd like to find a corresponding set of voxel indices in the cropped rawavg.mgz. Does FreeSurfer store any information related to the cropping that is done, I expect that there is only a translational shift in the SI axis but I'd like to automatically extract this value for each individual I've run through recon-all.
Thanks, Jerrold Jeyachandra