External Email - Use Caution I want Susceptibility Weighted and T1 weighted MRI scans for neurological disorder. Any help how we can get the data. Please help us out.
On Sat, 17 Jul 2021, 3:29 pm AmirHussein Abdolalizadeh, < amirhussei...@gmail.com> wrote: > 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://secure-web.cisco.com/1nQ6yiGbUs6UD1UqIlaYQQ0NiCmzguw3rYh290SVbb_9szd0a-j_MZFjW1kSFY6x8dhPKkseJ4NO0swS7gtmKFBsRBLIO7QGL_QYorbMc0Aa5Ftj7IFK0WkRtgiREmpJE_Jd0Qe97SA1bUUyxPS594u3IDkLLjNFZvJIZtXpfUXnI4K6QRcwf8I2ib1kWr8wKxALsjKBVN25PCrrAUZpZlNR7OsmoxWun3zpwVzGtlWYK6J-ndjyCUYNdSMJr1Zv26cBLEfBFQPVcRIKvGF1zOw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
