Hi Yanbin,

Are you still trying to solve this problem?

Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yanbin Niu niuyanbin365@gmail.com Sent: Wednesday, October 11, 2023 10:22 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Infant_recon_all generated surface does not align well with the provided aseg file

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Hi Freesurfers,

I'm currently working on running infant_recon_all with our edited aseg.nii.gz for newborn data. However, we've encountered an issue where the generated surface does not align well with the provided aseg file. I have attached some screenshots as an example, in which a fold that infant_recon_all is failing to fully recognize. This problem seems consistent across the brain and subjects.

I'm reaching out to inquire if anyone has experience with this issue and if there are specific parameters that we can adjust to address this issue.

Here is the command we've been using: infant_recon_all --s sub-1041 --age 1 --inputfile ${SUBJECTS_DIR}/sub-1041/mprage.nii.gz --segfile ${SUBJECTS_DIR}/sub-1041/aseg.nii --masked ${SUBJECTS_DIR}/sub-1041/brain_mask.nii.gz

Thank you, Yanbin Niu