Thanks for the suggestions.
Yeah, I converted the Canonical T1 template from SPM with the Analyze format to AFNI format. The dimension of the T1 template is 91*109*91, when I used the to3d command (to3d T1_template.hdr), I basically changed the field from 240 to 182 to give the voxel resolustion to 2*2*2 mm, but I left the origin of the image to the center (e.g. I did not touch the origin setting).
The EPI images I have is a 3d+t series, I have done all the preprocessings in SPM enviroment. since it has 41*48*35 dimension and the voxel size is 4*4*4 mm. I used the to3d command like this:
to3d -time:zt 35 imagenumber TR zero -prefix AFNIepi swaf*.hdr
NO GUI poped up here, the to3d program automatically genereate ANFNIepi+orig.BRIK and AFNIepi+orig.HEAD files. When I used 3dinfo command to look at this dataset, the field of view is 164mm (41*4), and origin is the center of the 41*48*35 dimension matrix.

Then After I opened AFNI gui, and define T1+orig as underlay, and AFNIepi+orig as overlay, they did not match with each other although they did when they are in the Analyze format.

One thing I noticed is that when I ued to3d command, the program did not really transfer the origin information to AFNI format correctly. Am I right on this issue? or do we have to manully specify the origin of the image? Can to3d program automatically read the origin information from Analyze format *.hdr file?


Any further suggestions are really appreciated!