Problem with REST slice viewer

Dear all,

I would very much appreciate your help with the following:

I would like to create images for publication using REST slice viewer, but encounter the following problem: if I use SPM's T1 template as underlay for my functional overlay, it works. However, if I try using the normalized T1 composite of my subjects as underlay, the overlay is then misplaced slightly outside of the brain. I do not have this problem when inputting both images in MRICron.
Would anyone have any ideas on why this is happening and how to fix the problem?

Thank you very much.


I guess this problem is caused by the rotation matrix with your T1 image or functional image.

REST slice viewer can not deal with images with rotations currently.

You can try:
2. Program for re-orienting the un-normalized image (diagonalize the complex affine matrix): y_reorient.m
to remove the rotation matrix.

I am not sure if it works.