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

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

External Email - Use Caution

Attached is the recon-all.log file. Thank you for your help

On Thu, Nov 16, 2023 at 4:57 PM Carlos Alcocer cda33@cornell.edu wrote:

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