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questions > RE: dcm2niix reorients all images to RPI, origins are changed
Feb 20, 2019 03:02 PM | Virginia Flanagin
RE: dcm2niix reorients all images to RPI, origins are changed
Hi,
I am having a similar issue. I have T1 images (MP-RAGE, SIEMENS) that were collected Sagittal RL, and when I convert them, the orientation is correct, but when I read them in (e.g. Slicer) then the slices are Axial IS. Keeping them in Sagittal RL is the easiest way to keep my transformation pipeline intact and reference everything to my T1 and B0.
I have changed the things that you suggested in this feed and recompiled the scripts but I still get the change from Sagittal to Axial. I am assuming this is because of the way that the NIFTI files save the data, that the whole system is in RAS or LPS such that the first dimension of the data is right/left etc.
Still, is it possible to change this?
Thanks,
Virginia
I am having a similar issue. I have T1 images (MP-RAGE, SIEMENS) that were collected Sagittal RL, and when I convert them, the orientation is correct, but when I read them in (e.g. Slicer) then the slices are Axial IS. Keeping them in Sagittal RL is the easiest way to keep my transformation pipeline intact and reference everything to my T1 and B0.
I have changed the things that you suggested in this feed and recompiled the scripts but I still get the change from Sagittal to Axial. I am assuming this is because of the way that the NIFTI files save the data, that the whole system is in RAS or LPS such that the first dimension of the data is right/left etc.
Still, is it possible to change this?
Thanks,
Virginia
Threaded View
Title | Author | Date |
---|---|---|
Angela Zhang | May 24, 2018 | |
Chris Rorden | May 24, 2018 | |
Angela Zhang | May 24, 2018 | |
Chris Rorden | May 24, 2018 | |
Angela Zhang | May 24, 2018 | |
Virginia Flanagin | Feb 20, 2019 | |
Chris Rorden | Feb 20, 2019 | |