Dear Afni experts,
I'm trying to combine motion correction from 3dvolreg and deformation correction from 3dQwarp (with the -plusminus option for the use of a reference with a reversed phase encoding direction (blip up and blip down)) in one interpolation step with 3dNwarpApply.
I would have expect that applying the correction sequentialy of simultaneously would yield very similar images, with the former only very slightly blurred, but I see what seems to be a rotation between the two. Here is a sample of the code used:
# Compute motion correction
3dvolreg -prefix trun01_mc.nii.gz -base mcTarget.nii.gz -1Dmatrix_save mcMatrix_run01 trun01.nii.gz
3dTstat -mean -prefix trun01_mc_mean.nii.gz trun01_mc.nii.gz
# Compute deformation correction
3dQwarp -prefix trun01_mc_mean.nii.gz -base deformationRef.nii.gz -weight brainmask.nii.gz -source trun01_mc_mean.nii.gz -noZdis -noXdis -plusminus -superhard -minpatch 9 -nmi
# Apply motion and deformation correction
3dNwarpApply -prefix trun01_mdc.nii.gz -source trun01.nii.gz -nwarp 'IS:trun01_mc_mean_PLUS_WARP.nii.gz' -affter mcMatrix_run01.aff12.1D -interp cubic
3dTstat -mean -prefix trun01_mdc_mean.nii.gz trun01_mdc.nii.gz
# Visual inspection
fslview trun01_mc_mean_PLUS.nii.gz trun01_mdc_mean.nii.gz
The rotation I see between trun01_mc_mean_PLUS.nii.gz and trun01_mdc_mean.nii.gz is about the x axis (RL). I was initialy not using the 'IS:' option, but it was the same.
I must be doing something wrong, but I cannot figure what.
Thank you very much in advance for helping me to sort that out!
Sebastien
