Hi Amir - Are you using the official 7.1.1 FreeSurfer release or a beta version? The config file that you are using seems to be newer than 7.1.1. Please attach your entire trac-all.log file, this will help answer this and other questions.

Thanks,
Anastasia.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh <amirhussein.a@gmail.com>
Sent: Saturday, July 17, 2021 5:57 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] dwi_orig_las issue trac-all -prep
 

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Dear FreeSufer users/experts,

I am trying to do TRACULA (FS 7.1.1) on a subject with b = 0,1000 in 60 directions. The preprocessing steps of denoising, bias-field, eddy/motion correction were done using MRtrix (in .mif format) and their outputs are converted into .nii, .bvec, and .bval. I changed the dmrirc.example into the attached file to omit the associated preprocessing steps.

Running the trac-all -prep -c dmrirc.pilot results in an error right at the beginning:

reading info from /<a long path!>/AnalyzeDWI/pilot/dmri/dwi_orig_las.1.nii.gz...
error: niiRead(): error opening file /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.1.nii.gz

It is not present in the output folder.

Interestingly, this file is generated a few lines above and then renamed into dwi_orig_las and then into dwi.nii.gz:
mv -f /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.1.nii.gz /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.nii.gz
A few lines later:
mv -f /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.nii.gz /<path>/AnalyzeDWI/pilot/dmri/dwi.nii.gz
Thus, my guess is due to this renames it cannot find it.

Any help is appreciated.

Bests,
Amir

p.s. the MRtrix-preprocessed file is itself LAS:
orientLAS /<path>/AnalyzeDWI/pilot/dmri/dwi_orig.1.nii.gz /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.1.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -8