DICOMs may save each slice or each volume separately. This is not a problem per se, it's just a format, but it suggests that something may have changed in the protocol, which begs the question if other things changed in the protocol. I'd start by checking the converted nifti (dmri/dwi.nii.gz) to see if it's different than the others in an obvious way, then checking the gradient table (dmri/bvecs) and b-value table (dmri/bvals) to see if each of them has as many lines as volumes in the nifti.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@icahn.mssm.edu>
Sent: Wednesday, May 13, 2020 7:36 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] trac-all prep error
 

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Hi, 

I have an error message when processing trac-all prep. attached the log file. 
error:
"terminate called after throwing an instance of 'std::logic_error'
  what():  Mat::operator(): index out of bounds"

Recon-all was finished without error. However, my raw DTI DCM file is 120 compared to others with over 2000 slices. Would that be a problem?

Best, 
Qi 

--

Ph.D. candidate 
Icahn School of Medicine at Mount Sinai