Transformation On PointSets (-rs)

[faeze-el]

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]

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 ***@***.***> 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* — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJPEW25APGEGMMHHTYFB43R4WCL7ANCNFSM4PDRGQEQ> .

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

[faeze-el]

thanks @pyushkevich for quick reply.
I tried this:
greedy -d 3 -rf fixedImg.nrrd -rs MovingImg.vtk vtkresult_affine.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)