Hi Michael
that looks pretty bad! What is the resolution of the T2? The T1 that you
overlay on also looks somewhat blurry - what was it?
Bruce
On Fri, 27 Sep
2013, Michael Waskom wrote:
Hi, just to make the problem a bit more transparent, I took a second
screenshot of the slices with the pial surface from the -T2pial run in red
and the pial surface from the normal run in
cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom <mwas...@stanford.edu>
wrote:
Hi,
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
----------------
https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt
Without -T2pial
--------------------
https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt
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
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