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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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