Hi Barbara - It's converting to LAS orientation. If it the images are already in LAS orientation, that command will have no effect, as you say.
a.y
On Fri, 17 Oct 2014, Barbara Kreilkamp wrote:
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
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