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Author: Chad (---.69-129.unk.tds.net)
Date: 03-19-07 14:00
Hi,
I've got some coronally acquired data -- a T2 FLAIR and a Tensor file. If I do a quick to3d (following), the FLAIR looks fine, but the tensor is inverted A-P.
to3d -prefix flair ../images/flair/IM*
to3d -time:zt 40 52 7000 alt+z -prefix grads ../images/dti_coronal/IM*
If I actually go into the DICOM headers and figure out the FOV values and enter them in, everything works out okay:
to3d -xFOV 126.31R-113.69L -yFOV 129.09S-110.91I -zSLAB 55.17P-100.83A -prefix flair2 ../images/flair/IM*
to3d -xFOV 126.31R-113.69L -yFOV 129.09S-110.91I -zSLAB 55.17P-100.83A -time:zt 40 52 7000 alt+z -prefix grads2 ../images/dti_coronal/IM*
In this case, flair2+orig is exactly the same as flair+orig. grads+orig is inverted A-P from grads2+orig. Interestingly, if I do
to3d -xFOV 126.31R-113.69L -yFOV 129.09S-110.91I -zSLAB 100.83A-55.17P -time:zt 40 52 7000 alt+z -prefix grads3 ../images/dti_coronal/IM*
then grads3+orig is exactly the same as grads+orig. So, it appears that the orientation AFNI determines itself if the FOV values are missing is backward from what it seems they should be.
I would guess if I sorted the images backward from how they were acquired, AFNI might figure things out correctly, but I'm curious if anyone knows why it can't determine this as is? Do I need to sort the images from last to first if the orthogonal vector is negative and first to last if it is positive or something?
Many thanks,
-Chad
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Determining Orientation of Siemens Mosaic new |
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Chad |
03-19-07 14:00 |
