Hello, I just found this list and I have a question about reorienting images using the display button's options in the graphics window.
I am following the SPM course videos, in particular, the preprocessing demo by John Ashburner. In the first part, he talks about reorienting images. I tried to follow the procedure on my own dataset, and I reoriented them by the same degree. I used the Check Reg on the reoriented T1 anatomical image and the T1 template provided by SPM, the images aren't aligned properly. The cross-hairs aren't placed in the same region of the brain on both images (T1 anat and T1 template), and the anterior part is clipped in the axial view of the T1-weighted anatomical (screenshot attached), though the T1 template is displayed fine. Can anyone please explain to me what am I doing wrong?
Also, how will this affect downstream preprocessing? I have used Dcm2nii for converting all the files into .nii files. Do I have to line up the 000 coordinates to the anterior commissure for every one of my scan sessions (each with one T1 anatomical multiple fMRI runs)? Thanks!
- Ananth
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