Hello,
I'm seeking advice regarding some difficulties I've had with
retrospective data. As part of our interest is using the images with
FreeSurfer, I've read with interest the documentation on FSL and
FreeSurfer. We are also interested in using BET as part of an
anonymization process. I am working with 3 datasets all collected on a
GE 1.5 T using Signa 4.05. All three were SPGRs, with two collected
sagittally (one elderly and one young subject) and one collected
coronally (elderly subject). Because I've run into some difficulties in
getting FreeSurfer to properly skull-strip and segment white matter, one
suggestion has been to use BET to remove the skull before processing in
FreeSurfer. BET has been somewhat successful, but it has a tendency
with these images to leave behind the much of the jaw and neck,
particularly if I relax the threshold to 0.3 - 0.35 to ensure an intact
brain (otherwise it tends to remove too much from superior parietal
areas). The coronal subject looks far worse, however, possibly due to
image quality. I tried using the -g option to adjust the gradient, but
it seems to work anterior to posterior, rather than top down as
suggested in the help file. I've also used avwswapdim to rotate the
images to that suggested in the FSL with FreeSurfer documentation, but
that does not appear to improve the problem; it still seems to adjust
the gradient anterior/posterior. Any ideas on what might be causing the
problem and how to solve this?
Incidentally, after using BET FreeSurfer improves its surface detection
with the two sagittal images but not the coronal one.
Thank you.
Amanda Bischoff-Grethe, PhD
Post-Doctoral Fellow
Laboratory of Cognitive Imaging
VA San Diego Healthcare System
3350 La Jolla Village Drive, M/C 151A1
San Diego, CA 92161
Phone: 858/552-8585 x1120 (Lab)
Fax: 858/642-6393
|