I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh.

However, I've found that using the T2 is causing rather dramatic problems with the pial surface.

I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log:

With -T2pial

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https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png

Without -T2pial

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https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png

The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface.

Any ideas?

Michael