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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.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.
