Hi-

If the data are in the same spot, and you *only* want the data orientations to match, then you can run 3dresample.

You could change one dset orientation to match that of the other, or change both to something nice like RAI (I am using made-up input and prefix file names here...):

3dresample -prefix MAG_RAI.nii.gz -orient RAI -input DSET_MAG
3dresample -prefix CEST_RAI.nii.gz -orient RAI -input DSET_CEST

After this, the datasets should appear in the same locations in the GUI (that is, nothing with coordinates will have changed), but now the orientation of the data stored on disk should match (RAI in both cases); you can verify this with:

3dinfo -orient -prefix MAG_RAI.nii.gz CEST_RAI.nii.gz

To perform alignment---yes, you can do that with our alignment programs. Many people have partial data to align to whole brain, and it can be done. There are details that matter though: do the two dsets have similar or opposite tissue contrast (--> determines what cost function to use)? Do they start off close-to-well-aligned or not (---> getting to a good starting point is nice, as there is less chance of a dset wandering off into space accidentally)?

For the second point here, what does the output image:

@djunct_overlap_check -ulay MAG_RAI.nii.gz -olay CEST_RAI.nii.gz -prefix image_mag_cest

look like? (It will show how well the dsets overlap to start.)

--pt