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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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