Hi Mackenzie

This is almost certainly an error in the spherical registration. You can try Andrew Li's JOSA algorithm, which is likely to fix this. Andrew: can you provide directions on how to run JOSA in the current recon-all?

Cheers Bruce From: Mitchell, Mackenzie macmitch@illinois.edu Sent: Tuesday, August 4, 2026 8:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Misidentification of the central sulcus in fsaverage registration

External Email - Use Caution Hello,

We are seeing that in some cases (13/167 subjects) FreeSurfer v7.3.2 incorrectly labeled the central sulcus in at least one hemisphere (see example below). In all cases, FreeSurfer is labeling the postcentral sulcus as the central sulcus. In one case, this is happening twice for the same subject who participated in two independent projects (i.e., we find this issue with different T1s and Freesurfer runs). See example below.

[HUBS05_RH_looksincorrect.png]

We have checked the segmentations and alignments for all subjects and they all look correct. We think this may be happening at the stage of normalization to fsaverage.

Most critically for us, it looks like this error is displacing the mapping of our functional data to the surface, as the motor network functional connectivity maps are shifted forward, as would be expected from the mislabeling. See example below.

[Bilateral motor FC.png]

In an attempt to resolve this issue, we have run FreeSurfer v8.2.0 on these 13 subjects. This resulted in the central sulcus being correctly identified in only 4/13 subjects.

Searching through past posts to this mailing list, we found this thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70250.html) which suggested to rotate the spherical registration (e.g., z+15 degrees). We found that with various rotation parameters we could improve the cortical parcellation in a handful of subjects. However, we do not currently use the cortical parcellations for our work and our primary concern is being able to accurately map functional data to the surface. We are not sure if spherical rotation is the right point/method to intervene.

All insight on how to intervene to improve fsaverage normalization would be greatly appreciated.

Thank you, Mackenzie

External Email - Use Caution

Hi Madison, Bruce, and Andrew,

I also have been looking at this issue, since most of the labs I work for use Freesurfer parcels as features in machine learning models.

I'm adding to these slides as I learn more about the issue:

https://secure-web.cisco.com/1KhR48Qvp4KsN3QfBMwFogNHJ4HrbBdH0dka_i8wA3EYk_6...

We greatly appreciate your help.

Donna

________________________________ From: Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Sent: Tuesday, August 4, 2026 10:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Li, Jian,PhD JLI112@mgh.harvard.edu Subject: [Freesurfer] Re: Misidentification of the central sulcus in fsaverage registration

Hi Mackenzie

This is almost certainly an error in the spherical registration. You can try Andrew Li’s JOSA algorithm, which is likely to fix this. Andrew: can you provide directions on how to run JOSA in the current recon-all?

Cheers

Bruce

From: Mitchell, Mackenzie macmitch@illinois.edu Sent: Tuesday, August 4, 2026 8:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Misidentification of the central sulcus in fsaverage registration

External Email - Use Caution

Hello,

We are seeing that in some cases (13/167 subjects) FreeSurfer v7.3.2 incorrectly labeled the central sulcus in at least one hemisphere (see example below). In all cases, FreeSurfer is labeling the postcentral sulcus as the central sulcus. In one case, this is happening twice for the same subject who participated in two independent projects (i.e., we find this issue with different T1s and Freesurfer runs). See example below.

[HUBS05_RH_looksincorrect.png]

We have checked the segmentations and alignments for all subjects and they all look correct. We think this may be happening at the stage of normalization to fsaverage.

Most critically for us, it looks like this error is displacing the mapping of our functional data to the surface, as the motor network functional connectivity maps are shifted forward, as would be expected from the mislabeling. See example below.

[Bilateral motor FC.png]

In an attempt to resolve this issue, we have run FreeSurfer v8.2.0 on these 13 subjects. This resulted in the central sulcus being correctly identified in only 4/13 subjects.

Searching through past posts to this mailing list, we found this thread (https://secure-web.cisco.com/1Av_o2jbMOBK2-QCYkM8TireDselI79riAZBd39wr1qcdaW...) which suggested to rotate the spherical registration (e.g., z+15 degrees). We found that with various rotation parameters we could improve the cortical parcellation in a handful of subjects. However, we do not currently use the cortical parcellations for our work and our primary concern is being able to accurately map functional data to the surface. We are not sure if spherical rotation is the right point/method to intervene.

All insight on how to intervene to improve fsaverage normalization would be greatly appreciated.

Thank you, Mackenzie

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