Dear afni experts:
I obtained the affine transformation between an epi and an anat T1 volumes using align_epi_anat.py. I then attempted to use 3dAllineate function to get an new epi volume that is aligned to the anat file. However, there is a relatively large displacement between the two files. I have some questions as follows.
1. I am not sure how to set the output grid (i.e., -master option for 3dAlineate) of the aligned epi file. If I choose the anat grid, it upsamples the epi volume because the anat vol has higher resolution. If I choose the epi source grid, it clips some epi data because of the large displacement. How can I get an aligned version of epi data without resample the data (i.e., same resolution)? I search a little bit and find that I can first run @Align_center. However, my epi volume has a narrow and a tilted FOV. So simply aligning grid centers or center of mass did not work very well...
2. My second thought is to create a new volume to serve as the master grid. I nudge the original epi file to roughly match the t1 file (i.e., remove the large displacement) and save this nudged epi. I then use 3dAllineate to transform the original epi to anat but set the nudge epi file as the grid such that I can preserve the grid resolution of the original epi. However, the clipping problem is even worse... Not sure why...
3. My third question is that, in my opinion, we do not even resample data at all when applying affine transform. For any epi file, you can simply use the affine transform and change the geometry info in the header file of the epi volume. In this way, no resampling will be executed. So I am confused about why we have to specify a master grid in 3dAllineate... Can I ask how to directly change the geometric string in an epi head file??
Sorry about the long question lists.
Ruyuan
