Hi ptaylor,
Thank you so much for your help!
+ the original coordinates are a bit odd-- while the anatomical and EPI overlay each other, the (x, y, z) = (0, 0, 0) location is far outside the brain; this can affect some alignment issues.
==> Do you have any idea of what could cause that in the aquisiton protocol?
I applied strictly your protocol, and it has improved the co registration of the anatomical images to the template. Thank you!
However, it's seems that volreg in align_epi_anat.py or more precisely 3dNwarpApply doesn't work when applying the parameters of @animal_warper. The result give an image that is not at all in the same space. Am I applying the good one?
# apply catenated xform: volreg/epi2anat/tlrc/NLtlrc
# then apply non-linear standard-space warp
3dNwarpApply -master anatT1_deob_warp2std_nsu+tlrc -dxyz 2 \
-source pb01.$subj.r$run.tshift+orig \
-nwarp "anatT1_deob_shft_WARP.nii.gz \
mat.r$run.warp.aff12.1D" \
-prefix rm.epi.nomask.r$run
Thank you again !