rawavg.mgz should have exactly the same dimensions as 001.mgz. orig.mgz
and downstream volumes will be cropped. Is that what you mean? To get
back to the native space, look at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 6/15/17 4:23 PM, Jerry Jeyachandra wrote:
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
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