It looks at the RAS of the direction cosines for the direction going from one slice to the next. If the absolute value of the R component is the max of the three, then it is assigned to be sagittal. If the A component is max, then it's coronal. If S, then axial
On 5/9/19 5:52 AM, falk.luesebr...@med.ovgu.de wrote: > External Email - Use Caution > > Thanks Doug, I think I may have resolved my orientation / transformation > issue. > > Do you happen to know how the primary slice direction is determined? > > Best, > Falk > > -----Ursprüngliche Nachricht----- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von Greve, Douglas > N.,Ph.D. > Gesendet: Freitag, 3. Mai 2019 17:31 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] Primary slice direction and image origin? > > You can get the image position from tag 20 32. It might not match what you > see in mri_info because we use RAS and dicom uses something else (LPS maybe), > so the "first voxel" might not be the same. > > > On 5/3/2019 3:01 AM, falk.luesebr...@med.ovgu.de wrote: >> External Email - Use Caution >> >> Hi Doug, >> >> thanks for your answer. I know how to print the slice direction, however, as >> there is no DICOM tag directly related to it, it has to be determined from >> some information of the DICOM header. I was wondering which these are. >> >> Same for the image origin or the voxel to ras transform in general: >> voxel to ras transform: >> 0.9367 0.0327 0.0240 -111.2289 >> -0.0206 0.8545 -0.4108 -82.6730 >> -0.0339 0.3843 0.9114 -121.5813 >> 0.0000 0.0000 0.0000 1.0000 >> >> In that transform the last column indicates the image's origin. However, I >> was unable to find the relation between the information available in the >> DICOM header and this transform. >> >> Best, >> Falk >> >> >> -----Ursprüngliche Nachricht----- >> Von: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von Greve, Douglas >> N.,Ph.D. >> Gesendet: Donnerstag, 2. Mai 2019 17:33 >> An: freesurfer@nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] Primary slice direction and image origin? >> >> You can use --slicedirection to get the slice direction (it will also get >> printed out by just running mri_info on a file). What do you mean by the >> image origin? >> >> On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote: >>> External Email - Use Caution >>> >>> Dear all, >>> >>> This is not directly related to FreeSurfer, however, can anyone tell >>> me how the primary slice direction and image origin is determined >>> from the DICOM header as displayed for example using mri_info? >>> >>> Best, >>> >>> Falk >>> >>> ............................................... >>> >>> klinikum_logo_schmal_e-mail_blau >>> >>> *Universitätsklinik für Neurologie* >>> >>> >>> Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät >>> Leipziger Str. 44 >>> 39120 Magdeburg >>> >>> *Telefon: *+49-391-6117-512 >>> >>> *falk.luesebr...@med.ovgu.de <mailto:falk.luesebr...@med.ovgu.de>* >>> *http://www.kneu.ovgu.de/kneu.html* >>> >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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
