Hi Bob,
I was looking at bilinear for eddy current correction to test against affine to see if it was much better or not. I ran into a strange problem. I ran the following:
ind=0
while [ $ind -le 60 ]
do
3dAllineate -base B0ref_resamp.nii.gz -source dwi.nii[$ind] -master BASE -prefix eddy_${ind}.nii -1Dmatrix_save dwi_${ind}.aff12.1D -1Dparam_save dwi_${ind}.param.1D -nwarp_save warp_${ind}.nii.gz -warp aff -nwarp bilinear

ind=$((ind+1))

done

NOTE:B0ref_resamp.nii.gz is a higher resolution (1.5mm iso) than the dwi set (2mm iso). I also have B0ref.nii.gz which is the same resolution as dwi (2mm).

When I use 3dAllineate -1Dparam_apply dwi_0.param.1D -nwarp bilinear -master B0ref.nii.gz -source dwi.nii[0] -prefix dwi.eddy.0_test.nii it looks perfect.


When I use 3dNwarpApply it looks very zoomed in compared to the original reference image and cuts the brain off:
3dNwarpApply -nwarp 'warp_0.nii.gz' -master B0ref.nii -source dwi.nii[0] -prefix dwi.eddy.0.nii

When I tried combining affine+nonlinear again the image looks zoomed in. Is there something that is wrong that I should change to get nwarp to work correctly? I also tried adding IDENT(B0ref.nii.gz) before and after the original try of using warp_0.nii.gz to see if resampling helps and it does not....any ideas?


I would eventually like to combine the bilinear warp field with a warp to MNI which is why I want to figure out how to use the nwarp option in 3dNwarpApply.

Thanks,
Ajay



Edited 2 time(s). Last edit at 03/21/2018 05:17PM by AjaySK.