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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh <amirhussei...@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 External Email - Use Caution 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.