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
Anastasia. ________________________________ 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
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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