When freesurfer reads in an img/hdr file, it makes assumptions about the how the data are oriented, so, implicitly, you are using orientation info. If you do not have a .mat file, then you can't change the header, so you have to change the pixels
On 05/09/2017 01:45 PM, Shane Schofield wrote: > Sorry, I don't quite understand yet.. Would the header be important as > I am not using img / hdr ? Under what sort of circumstances would pix > be favourable? I am using .nii after executing mri_convert to go from > img/hdr to nii. I note that pix is used in other older threads too. > > > On Tuesday, May 9, 2017 5:58 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: > > > When the pixel data are flipped, you are actually changing the way that > the data are stored on disk (while keeping the direction info in the > header constant). > > > On 05/09/2017 12:52 PM, Shane Schofield wrote: > > Dear Doug, > > I am trying to flip some PET images so that they are in the same > > orientation as the T1. > > I came across this post > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.html > > Can you explain what what it means to change the pixel data? Should I > > use pix or without pix? For context I am working with PET data (in > > img/hdr formats) that seemed to have been flipped L/R somehow. > > Thank you. > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto: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. > > > > > > > _______________________________________________ > 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
