Freesurfer August 2026

freesurfer@nmr.mgh.harvard.edu

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25 discussions

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recon-all-clinical pediatric ventricle segmentation
by Betz, Anja Katharina 05 Aug '26

05 Aug '26

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Trouble finding recent archives
by Dierker, Donna 05 Aug '26

05 Aug '26

External Email - Use Caution I'm having trouble finding the mailing list archives. This exists, but I can't find more recent messages: https://secure-web.cisco.com/1_AzCMVLSYPWXrEp1K-AJyCtXx9QQ9JDRC8EUf3bu9E09G… The archives link here says Forbidden: https://secure-web.cisco.com/1t7pgqdKCNN4T1zl63JGJU0ZpokAYt_RliqFTp2CWPt9AG… Thanks, Donna ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Question: Manual control points in FreeSurfer 8.2 are read as 0 points by mri_normalize
by Deborah Pou 04 Aug '26

04 Aug '26

External Email - Use Caution Hi, I am needing some help with control points. Environment: - FreeSurfer 8.2.0 - Ubuntu 22.04 on WSL2 I am trying to manually edit a subject using control points for intensity normalization. Workflow: 1. Open the subject in Freeview. 2. Create a new Point Set. 3. Save it as "Control Points" into: SUBJECT/tmp/control.dat 4. Run: recon-all -s SUBJECT -autorecon2-cp -autorecon3 The recon-all log shows: mri_normalize -f SUBJECT/tmp/control.dat ... using control points from file SUBJECT/tmp/control.dat... However, immediately afterwards it reports: Reading 0 control points... error: MRI3dGentleNormalize: mean = 0.0, nctrl = 0 The command completes, but the manually placed control points are ignored. As a verification, I compared the original and edited normalization volumes: mri_diff original/mri/norm.mgz edited/mri/norm.mgz Output: diffcount 0 which indicates that intensity normalization was unchanged. Am I doing something wrong? Is this the expected behavior in FreeSurfer 8.2, or is there an issue with how Freeview writes control.dat?

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Misidentification of the central sulcus in fsaverage registration
by Mitchell, Mackenzie 04 Aug '26

04 Aug '26

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/18f5PAXmePTLSv04gGyGwEsaY9MJkKjxLyhKbYkcEUbMBl…) 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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Request for FreeSurfer License for Academic Research Use
by bhwang1228 03 Aug '26

03 Aug '26

External Email - Use Caution Dear FreeSurfer Team, I am writing to request a FreeSurfer license for academic research use. I am a researcher working on neuroimaging analyses using UK Biobank brain MRI-derived phenotypes. The software will be used only for non-commercial academic research and data visualization purposes. Thank you very much for your help. Best regards, Binghan Wang

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Freesurfer August 2026