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pyushkevich / greedy

Very fast greedy diffeomorphic registration code
GNU General Public License v3.0
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Transformation On PointSets (-rs) #17

Open faeze-el opened 3 years ago

faeze-el commented 3 years ago

I used the following commands for registration and it worked perfectly. After that, I applied transformation (warp(affine)) on pointset like .vtk or .obj formats but there is a problem that the result (vtkresult.vtk) is exactly the same as MovingImg and it seems that the transformation doesn't have any effect on the MovingImg.vtk. Would you help me with applying transformation on pointset?

_greedy -d 3 -a -i fixedImg.nrrd MovingImg.nrrd -dof 12 -o affinematrix.mat -m SSD -ia-image-centers -n 100x0 -float greedy -d 3 -m SSD -i fixedImg.nrrd MovingImg.nrrd -it affinematrix.mat -o warp.nii.gz -oinv inverse_wrap.nii.gz -n 100x0 -float greedy -d 3 -rf fixedImg.nrrd -rm MovingImg.nrrd finalOutput.nrrd -ri LABEL 0.2vox -r warp.nii.gz affinematrix.mat -float__

before registration .nnrd images: https://drive.google.com/file/d/1UP0-A2XK2aumJQl1N0qR5_MsYO0KEep5/view?usp=sharing

after registration .nrrd images: https://drive.google.com/file/d/1e4lmPDTOqng6octnIxqDyCw2f8paalaz/view?usp=sharing

transformation on vtk: greedy -d 3 -rf fixedImg.nrrd -rs MovingImg.vtk vtkresult.vtk -r warp.nii.gz affinematrix.mat

pyushkevich commented 3 years ago

The -rs flag does not work great. Can you try with just the affine and see if that does anything?

On Tue, Jul 21, 2020 at 8:25 AM faeze-el notifications@github.com wrote:

I used the following commands for registration and it worked perfectly. After that, I applied transformation (warp(affine)) on pointset like .vtk or .obj formats but there is a problem that the result (vtkresult.vtk) is exactly the same as MovingImg and it seems that the transformation doesn't have any effect on the MovingImg.vtk. Would you help me with applying transformation on pointset?

greedy -d 3 -a -i fixedImg.nrrd MovingImg.nrrd -dof 12 -o affinematrix.mat -m SSD -ia-image-centers -n 100x0 -float greedy -d 3 -m SSD -i fixedImg.nrrd MovingImg.nrrd -it affinematrix.mat -o warp.nii.gz -oinv inverse_wrap.nii.gz -n 100x0 -float greedy -d 3 -rf fixedImg.nrrd -rm MovingImg.nrrd finalOutput.nrrd -ri LABEL 0.2vox -r warp.nii.gz affinematrix.mat -float_

before registration:

https://drive.google.com/file/d/1UP0-A2XK2aumJQl1N0qR5_MsYO0KEep5/view?usp=sharing

after registration:

https://drive.google.com/file/d/1e4lmPDTOqng6octnIxqDyCw2f8paalaz/view?usp=sharing

greedy -d 3 -rf fixedImg.nrrd -rs MovingImg.vtk vtkresult.vtk -r warp.nii.gz affinematrix.mat

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-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine

faeze-el commented 3 years ago

thanks @pyushkevich for quick reply. I tried this: _greedy -d 3 -rf fixedImg.nrrd -rs MovingImg.vtk vtkresultaffine.vtk -r affinematrix.mat But the "vtkresult_affine.vtk" is exactly the same as "MovingImg.vtk". I also compared them using notepad++.

Greedy Version 1.0.1, Release date: Mar 21, 2019. (the greedy.exe file on itk-snap 3.8)