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