After a quick test, I found a small problem of the second
WarpMultiTransform in reproduce3.sh. Here is the output:
Step 1 mni-anat:
/home/songgang/local/ANTS/gccrel_itk320/WarpImageMultiTransform 3
mni.nii.gz mni2anat-multi.nii.gz -R brain_avg.nii.gz
anat2mni_InverseWarp.nii.gz -i
If two images have different image headers, they are supposed to align
in the physical space, not in the image voxel space, for warping in
ANTS.
I noticed you used two different images as references. Could you try
both use -R epi_template.nii.gz and verify if this issue still exists?
This is very possible with using the mask. It can be better to include
some background.
Could you email me this pair of images and masks? I am very interested
to think about any way to improve upon this.
Thanks
-Gang
Quoting Michael Hanke michael.ha...@gmail.com:
On Thu, Jul 15,
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