All,

I have a question regarding the required registration file in mri_vol2surf.

I have some spherical ROI's in MNI space produced via 3dUndump--they're
volume files that show up in the correct places when loaded in with an
MNI standard subject such as fsaverage.

I also have some patients scans. I'd really like to compute cortical
thickness for these ROI's on my patient scans, so I attempt to follow
the instructions at (
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ),
but these instructions assume that the ROI is in the native space--which
produces no problems until the step :

cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf \
   --mov /path/to/ROI5.nii \
   --reg TT_avg152T1_to_fsaverage.dat \
   --projdist-max 0 1 0.1 \
   --interp nearest \
   --hemi lh \
   --out lh.fsaverage.ROI5.mgh \
   --reshape

My question is then three parts:

(1) Why does vol2surf require a registration file? Shouldn't it be
possible to do it as a straight conversion of data types if I know that
my surface is registered to the file that I want? Perhaps naive, my
first intuition was to construct a TT.dat that was the identity matrix,
but this fails, with the response listed in (2).

(2) How can I do this without shifting my data? If I follow the
instructions, when the surface is overlayed on fsaverage's lh.pial, the
entire surface is included in the overlay.

(3) What exactly do the numbers mean in the registration file TT.dat (as
in the instructions on the website)? The 4x4 matrix is clear, and the
first two numbers appear to have something to do with Voxel resolution,
but I'm unable to find documentation that explains the notation in the
output.

Any help anyone can offer would be tremendously appreciated.

-qf

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