Hi,

I'm frustrated the 3drefit function for a while:
I have a field map data (I extract magnitude(mag) image and the mag image 3dinfo showed orientation is SAR) and a CEST data (3dinfo showed orientation LSP) from rat brain and try to run the field map correction for the CEST image.
I resample them to 4x4x4 with
3dresample -dxyz 4 4 4 -prefix mag_res_brain444.nii -inset mag_res_brain.nii.gz
3dresample -dxyz 4 4 4 -prefix CEST_res_brain444.nii -inset CEST_res_brain.nii.gz
then the orientation of mag_res_brain444.nii from 3dinfo is still SAR (fig mag_CEST_info_1, whole brain image,mag_3dinfo)
and the orientation of CEST_res_brain444.nii from 3dinfo is still LSP (fig mag_CEST_info_1, 5 slices coronal image)
and the AFNI view of the two images show same orientation (fig mag_CEST_info_1 ) like raw images before 3dresample.

I used 3drefit to change the head file of mag_res_brain444.nii to LSP for CEST image is LSP orientation then align it to CEST image, but it failed.
3drefit -deoblique -epan -orient LSP -xdel 4 -ydel 4 -zdel 4 mag_res_brain444_1+orig
the mag_res_brain444_1+orig show [-orient LSP] but AFNI view show the orientation totally changed (fig mag_3drefit).
so, 1. why 3dresample made image to 4x4x4 but AFNI view of CEST_res_brain444.nii still show 20x20x4 like before 3dresample? how to fix it?
2. Why the AFNI view show the image orientation was changed if 3drefit only change the orientation information in head file? how to fix it?
3. Is this a right strategy to make 3dinfo and AFNI view consistent in mag and CEST then align the mag image to CEST?
Thanks a lot,
Tracy