Hi Jon,
I'll leave this to Krish, as he's the local expert on mris_volmask, but it definitely could. Do you want to upload an example of a subject that failed for us to try out?
Bruce
On Thu, 14 Apr 2011, Jonathan Winawer wrote:
Hmm. At least when I use tkmedit, the surfaces seem to be correctly registered to both the high resolution volume (rawavg.mgz) and the 1x1x1 volume (T1.mgz). So it does not look like a coordinate problem, at least to my un-expert eyes. But maybe tkmedit does a different transform of the surfaces than mris_volmask?
In any case, the failure of mris_volmask to produce a good ribbon file follows a very characteristic pattern that looks more like a topology confusion to me, as you can see in the attached png. I say this because voxels along the gray-white border are labeled white (with some gaps) and voxels along the pial surface are labeled as gray. Also, some of the regions which are unlabeled holes in the correct (original) ribbon become labeled islands in the new, high-res ribbon. So it looks like the surfaces are in the right place, but they are somehow not filled in correctly. This precise pattern happens with every high-resolution brain I use when I try to re-run mris_volmask. In contrast when I rerun mris_volmask on bert, it works perfectly, though in this case the rawavg.mgz is already registered to T1.mgz and has the same resolution.
Could a coordinate problem cause this?
Sorry for all the questions. I seem to be stuck though. Many thanks again for your quick responses!
Jon