Hi all,

I want to coregister an averaged DWI b0 image (left side in attachment) to a high-resolution image slab, that only covers the brainstem (right side in attachment) within subject. I unsuccessfully tried a combination of align_epi_anat and 3dresample.
E.g.
1.
align_epi_anat.py -overwrite -dset1 hires+orig. -dset2 anat+orig. -dset1to2 -dset1_strip None -edge -cost lpa
align_epi_anat.py -overwrite -dset1 b0+orig. -dset2 anat+orig. -dset1to2 -dset1_strip None -edge -cost lpa
3dresample -master hires_al+orig. -prefix b0_2_hires -input b0_al+orig.
2.
align_epi_anat.py -overwrite -dset1 hires+orig. -dset2 b0+orig. -dset1to2 -partial_axial -dset1_strip None -dset2_strip None -edge -cost lpa
3dresample -master hires_al+orig. -prefix b0_2_hires -input b0+orig.

But the resulting coregistered b0 image was always misaligned on the hires image after the resampling.

Your help here is highly appreciated.

Bests,
Philipp