NaNs are in your original input image. They are replaced with 0 in the output
mri/orig/001.mgz.
Doug mentioned “Sometimes SPM will put NaNs in the image to indicate a mask.”.
Is that your case?
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Carlos Alcocer
Sent: Tuesday, November 21, 2023 10:59 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all error
External Email - Use Caution
Reposting due to issue with email bouncing. I am receiving following error on
my subjects. Recon-all still continues after error and finishes "without error"
I have attached the recon-all log as well.
mri_convert /path/to/inputt1.nii /path/to/mri/orig/001.mgz
mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz
reading from /path/to/anat_t1.nii...
NaN found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...
Thank you,
Carlos
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