Dear all,
Would you please explain why TRACULA is flipping the data so often? And what does the flip4fsl command do? The data I have is already in the right (radiological) orientation. fslswapdim does not seem to have an effect either, as the parameters are just set to 'x y z'. Are these commands only effective if the data is not in radiological convention?
Thank you, Barbara
flip4fsl /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig.nii.gz/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -5.02198 fslswapdim /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig.nii.gz x y z /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz