Jun, the "--out_orientation" is probably not what you want. As the documentation says,
NOTE: THIS IS ONLY TO BE USED WHEN THE ORIENTATION INFORMATION IN THE INPUT FILE IS *WRONG*. IF IT IS CORRECT, THIS WILL MAKE IT WRONG! if you're starting with dicom, it is very probably right. Is there a reason you think it would be wrong. What are you trying to do? doug Xu, Jun wrote: > > Hi, > > I was trying to create affine matrix from DICOM file and compared with > the one created by mri_convert. > > For T1 image, if I use mri_convert > > >mri_convert –it dicom [in filename] –ot nii [out filename] > > The affine matrix (srow*) part get from load_nii_hdr.m command is > > Affine I: > > srow_x: [0 0 -1.2000 92.2031] > > srow_y: [-1 0 0 132.7965] > > srow_z: [0 -1 0 131.8291] > > which is the same affine matrix I got directly from DICOM file > according to the description in nifti header doc. > > *However,* if I use > > >mri_convert –it dicom [in filename] –ot nii [out filename] > –out_orientation PRS > > The affine matrix (srow*) part get from load_nii_hdr.m command is > > Affine II: > > srow_x: [1 0 0 -123.7969] > > srow_y: [0 -1 0 140.7965] > > srow_z: [0 0 1.2000 -92.1709] > > That I do not know how to create. I know the orientation is changed > from PSR (T1 sag original) to RPS (specified in out_orientation). > Could you tell me what I can do in order to obtain > > an affine matrix II from affine I? > > Thanks. > > Jun > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list [email protected] 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.
