Dear AFNI experts,

I am using 3dNwarpApply (from afni 18.1.26) to unwarp an EPI image and move to the space of structural scan via another structural scan .

my command looks like that :

3dNwarpApply -source myepi.nii.gz -prefix epi.REG2SWI.nii.gz \
-master myswi.nii.gz \
-nwarp " UNI2SWI.txt epi2UNI.txt 03_epi_MidWarped_Forward_WARP.nii.gz"

Given that all my EPIs have a partial coverage I found it much easier to do the registration with itksnap and then convert the affine to the afni format. So I

1) Unwarp my EPI with unWarpEPI.py and register it to the MP2RAGE
2) Register the SWI image to the MP2RAGE
3) I run 3dNwarpApply in order to avoid multiple interpolations

If I simply concatenate my two affines and use 3dAllineate the registration works (so I think all my affines are in the right format) and the final volume is not cropped.

When I use 3dNwarpApply in two (out of 10 subjects) the final volume is cropped.

Before the whole process starts I use @Align_Centers to move all my volumes to the center of the MP2RAGE.

I tried to use 3dZeroPad on the -master myswi.nii.gz, but the final volume is still cropped.

Am I doing something silly? I am surprised that I get this issue only in 2/10 subjects which makes it more difficult to understand what the problem might be,

Any help would be much appreciated,

Best Regards,

Marcello