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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

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