Hi Pedro
they should be based on the input to mris_make_surfaces, which I believe
is brain.finalsurfs.mgz
cheers
Bruce
On Tue, 17 Mar 2015, Pedro Rosa wrote:
Hi, Bruce.
I tried several thresholds in some subjects and it seems to work reallh well.
Thanks for the help!
However, I would like to ask whether I should determine the expert values based
on the raw image (001.mgz) or the normalized image (T1.mgz)? I am asking this
because I believe the normalization can change the intensity values a lot.
Thanks again,
Pedro.
On Feb 18, 2015, at 19:58, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
can you check mri_segmet and mris_make_surfaces and see if the auto-detected
intensity parameters are reasonable? Things like max gray at csf border and
such. If not, you can set them explicitly using the expert opts - this usually
works
Bruce
On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote:
Hi,
I am resending it once I could not find it in the archives.
Thanks,
Pedro.
Dear Freesurfers,
I am working on a 1.5T MPRAGE sample of first-episode psychosis and controls,
and have found that some subjects end up having thin cortical surfaces with
frequent unsegmented deep sulci. I think this was worse with FreeSurfer 5.3
than with FreeSurfer 5.1. I attached some screen shots of aparc+aseg labeling
T1.mgz from a few of these subjects.
This seems to be a widespread cortical issue, although it was heterogeneous across
subjects (some of them seemed to have the “caudal half" of both hemispheres
adequately segmented), and trying to simply rerun those subjects was not very
helpful. Should I manually work on them, rerun recon-all with distinct parameters,
or just discard them?
Regards,
Pedro Rosa.
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