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
