Hi Yanbin,
Are you still trying to solve this problem?
Lilla
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yanbin Niu
<niuyanbin...@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
External Email - Use Caution
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
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