Is the T2 aligned with the T1?
On 7/7/2020 4:53 PM, Iglesias Gonzalez, Juan E. wrote:
Dear Jenna,
1.Manually editing aseg.mgz fixes the initialization (super important).
2.Manually editing wmparc.mgz fixes the intensity priors (less
important, but still important)
If it’s only 1 subject in a bigger study, I’d probably call it a QC
fail and leave it out.
If it’s a single case you’re very interested in, I would edit both
aseg.mgz and wmparc.mgz (you can copy the hippocampus from one into
the other, but you still need to fix the surrounding labels).
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jenna
Katherine Blujus <jkblu...@uwm.edu>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Tuesday, July 7, 2020 at 16:24
*To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
*Subject: *[Freesurfer] Freesurfer Hippocampal Subfield Misalignment
* External Email - Use Caution *
Hi Experts,
I ran the hippocampal subfield segmentation protocol using a T2 image
that does not cover the whole brain in Freesurfer v6.0. I noticed that
the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical
boundaries of the hippocampus in some of my subjects is off. For
example, the left hippocampal subfield segmentation in one subject is
superior and medial to the hippocampus. I checked the aseg.presurf
file (since I am using v6.0) and indeed the whole left hippocampus is
off.
I saw in a previous thread
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23942.html)
that it was suggested to edit the hippocampal segmentation within the
aseg file to potentially improve alignment of the subfield
segmentation. However, a more recent post
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54543.html)
stated that both the wmparc.mgz and aseg.mgz files would need to be
edited and that this was not recommended. Do you have any
recommendations on how to move forward? I did edit the hippocampal
segmentation within the aseg.presurf file in one of my subjects and
reran the subfield segmentation command which substantially improved
the output (i.e., it overlays on the hippocampus after correction).
Would you suggest that I continue with editing the aseg using
previously published protocols on segmenting the hippocampus by hand
or would you recommend something else?
Thanks in advance!
Jenna
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