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.htmlCan 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.
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.
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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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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