And how did you create 001.mgz? Sometimes SPM will put NaNs in the
image to indicate a mask.
On 11/17/2023 10:12 AM, Huang, Yujing wrote:
Hi Carlos,
Can you attach recon-all.log?
Best,
Yujing
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer
*Sent:* Thursday, November 16, 2023 4:57 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] recon-all error
* External Email - Use Caution *
Hi,
For some of my subjects I get the following error at the beginning of
recon-all:
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...
However, recon-all will keep running and then later finish without
error. What exactly is going on? This is only happens on some subjects.
Thank you,
Carlos
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