Hi Rita - From the log file, the first error occurs when it tries to convert your DWI nifti volume to LAS orientation:

mri_convert -oni 128 -onj 128 -onk 62 -oid 0 0 0 -ojd 0 0 0 -okd 0 0 0 -oc -2 24 35 -rt nearest /home/rita/Desktop/test/diffusion_output/MRI_20160226_2_PHD003/dmri/dwi_orig.nii.gz /home/rita/Desktop/test/diffusion_output/MRI_20160226_2_PHD003/dmri/dwi_orig_las.nii.gz

mri_convert: directions must have non-zero magnitude; out_i_direction = (0, 0, 0)

Is there something up with the header of your nifti? What do you see when you run this command?

mri_info /home/rita/Desktop/test/diffusion_dcm/MRI_20160226_2_PHD003/MRI_20160226_2_PHD003_dwi.nii.gz

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rita Vieira <ritagonvieira@gmail.com>
Sent: Wednesday, March 3, 2021 1:12 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA preprocessing errors: cannot create dwi_orig_las.nii.gz

External Email - Use Caution

Dear FreeSurfer experts,

I am a new user of FreeSurfer and I am trying to apply TRACULA to my data. However, I am stuck in the pre-processing part.

I have the following error at the end:

ERROR: Transform file should be eddy_correct/eddy log file or .mat file

But, the problem starts early because it cannot create the dwi_orig_las.nii.gz file.

Also, the bvecs.norot is filled with zeros.

I checked the bvals and bvecs file and they follow the format required by TRACULA.

In attachment, you can find the configuration and trac-all.log files.

Thanks in advance!

Rita