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Hello, There is of course the *last resort* of deleting the orientation and re-assigning it. This (as mentioned on FSL's pages) is generally a last resort, as getting the L-R orientation can be very difficult. If your subjects have a marker to indicate LR, this can be a rather simple method. See fslswapdim and fslorient, if interested. http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils On Sun, Nov 2, 2014 at 4:17 AM, elahe' yargholi <[log in to unmask]> wrote: > > Thanks. > I read its manual, it only speaks about converting dcm to nii, but my main > problem is converting 1142 3D nii images to 4D nii. Any suggestion? > > > I do appreciate your attention. > > BR, > Elahe' > > On Sun, Nov 2, 2014 at 10:01 AM, Stephen Smith <[log in to unmask]> > wrote: > >> Hi - try Chris Rorden's latest and greatest conversion tool: >> >> https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage >> Cheers >> >> >> On 2 Nov 2014, at 05:07, elahe' yargholi <[log in to unmask]> >> wrote: >> >> Dear FSL experts, >> >> I usually use mricron to convert dicom images to 4D nii, but this time my >> 4D data has 1142 volumes and mricron did not work so used mri_convert or >> unpacksdcm from freesurfer. They produced the 4D data, but the >> anterior-posterior is (left to right) in opposite direction of previous 4D >> data or MNI atlas and the fsl registration is incorrect. what is the safest >> way to correct that? >> >> >> >> I do appreciate your attention. >> >> BR, >> Elahe >> >> >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >> >> --------------------------------------------------------------------------- >> >> Stop the cultural destruction of Tibet <http://smithinks.net> >> >> >> >> >> >