Hi Carl
This happens in a small fraction of cases that have an outlier folding pattern
(an extra fold) in perirolandic cortex. You can fix it by manually drawing a
central sulcus label on the surface, saving it, then rerunning mris_register
witih (from the help):
-L <labelfile atlas_gcsa_file label_name>
Specify a manual label to align with atlas label <label name>
The label is the one you created, the atlas would be the Destrieux one, and the
name has to match the central sulcus name in that atlas (S_central I think but
you can check in the colormap)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Trolle, Carl
Sent: Wednesday, July 6, 2022 10:51 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Shift in cortical parcellation, issues with previously
suggested solution
Dear FreeSurfer team,
1. We are attempting to compute the average cortical thickness for controls
and persons with a neurological condition. In some cases, we've noticed that
the pre- and post-central gyri have shifted in the anteroposterior direction so
that the left and right gyri are not aligned. A similar phenomenon has been
reported previously
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70316.html) and
solved. However, we get the following error when attempting the previously
proposed solution:
ERROR: Flag -nospherereg unrecognized
Are there any other solutions or suggestions for addressing this shift that may
work for us?
1. Also, if we are interested in analyzing the cortical thickness of the
entire hemispheres using the mri_glmfit-function and not comparing specific
ROIs directly, does the correct parcellation/labelling of specific ROIs matter?
Kind regards,
Carl
FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Platform: CentOS Stream 8
Screenshot: please see attached
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