I have been asked to use FreeSurfer to create a good brain
mask for use in another analysis stream (DTI and other
things). I have chosen to do this by running recon-all on the
structural scan, then taking the (aseg+aparc) and using FSL to
dilate and erode to fill holes. This I binarize and rotate
back into the same orientation as the original structural
volume, and finally strip the padding added by recon-all, thus
making the mask match the original T1 so it can be overlaid
properly.
The only problem is that, besides rotating and padding,
recon-all also resamples to exactly 1.0 isovoxel, whereas the
original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way
to undo this resampling. Best I can determine this happens in
the recon-all stream near the beginning where is seems to
create some Talariach transform.
Any ideas how to undo this xform, or can you suggest a
better way to accomplish my goal.
-Jeff Eriksen
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