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 greve@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 greve@nmr.mgh.harvard.edu mailto:greve@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