Problem with REST slice viewer

Submitted by opril on Fri, 12/02/2011 - 04:45

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.

Olga

Submitted by YAN Chao-Gan on Sat, 12/03/2011 - 10:53

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: http://restfmri.net/forum/Programs_YAN
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.