Do you not have the image in something other than analyze? If not, then just keep playing with the letters (ie, PIR) until you get it right. Note that you will not know what is left and right unless you have a fiducial on the subject doug
On 06/11/2015 04:19 PM, Kriegel, Jennifer Lynn Sarai wrote: > > I used the following command to convert a sagittal slice from analyze > to mgz format. The original was acquired in an anterior to > posterior/right to left angle of slices. However, while it is > converting to an mgz properly, it seems to be giving me a flip upside > down, and reverting to transverse orientation. How do I specify for > the sagittal slice? > > Thanks. > > $FREESURFER_HOME/bin/mri_convert \ > > $SUBJECTS_DIR/fmri35_MPRAGE_o17/fmri35_MPRAGE_o17_0001.img -it analyze > --in_orientation PIR \ > > $SUBJECTS_DIR/fmri35_o17/mri/orig/001.mgz > > - Jennifer Lynn Sarai Kriegel > > MS in Psychological Sciences, Cognition and Neuroscience Emphasis > > Functional Neuroimaging of Memory Lab, Center for Vital Longevity > > The University of Texas at Dallas > > jlk130...@utdallas.edu <mailto:jlk130...@utdallas.edu> > > ------------------------------------------------------------ > > I am looking for a lot of men who have an infinite capacity to not > know what can't be done. > > - Henry Ford > > The important thing is not to stop questioning. Curiosity has its own > reason for existing. > > - Albert Einstein > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
