2D to 2D DIR for cine MRI

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Lena Nenoff

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Aug 24, 2023, 11:15:59 AM8/24/23
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Dear plastimatch community, dear Greg,

we are trying to register 2D images from cine MRIs. We use the setting you recommend for 2D registrations in http://plastimatch.org/batch_registration.html

[GLOBAL]
fixed=FIXED
moving=MOVING
img_out=WARPED
vf_out=VF

[STAGE]
xform=bspline
res=1 1 1
grid_spac=4 4 4
regularization_lambda=0.1
max_iterations=11

unfortunately it breaks right after entering the registration stage without an error notice: 

Doing registration stage

[1] xf_in->m_type = 0, xf_out->m_type = 0

RESAMPLE 0 1: (3 3 1), (3 3 1)


if we change the implementation to   impl=itk we get a different error:

Starting ITK registration
Exception caught in itk registration.

 itk::ExceptionObject (00000084652FF2D0)

Location: "unknown"

File: c:\users\grego\build\src\insighttoolkit-4.13.2\modules\filtering\imagefilterbase\include\itkRecursiveSeparableImageFilter.hxx

Line: 245

Description: itk::ERROR: RecursiveGaussianImageFilter(00000229A40181F0): The number of pixels along direction 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed.



We also tried changing the metric to 
metric=mi. This ran through, but all values were 0, even if the images were very different, so this didn't seem to have worked either.

Do you experience or an idea how to circumvent that?

Thank you very much for your help!
best,
Franciska and Lena

Franciska Lebbink

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Sep 4, 2023, 1:41:50 PM9/4/23
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Dear plastimatch community, dear Greg,

We got a bit further with the registration by applying a mask and changing some parameters for the stage. However, we have some holes in our registration. 
We used the following parameters: 
[STAGE]
xform=bspline
res=1 1 1
metric=mse
grid_spac=1 1 1
regularization_lambda=0.1
max_iterations=30

In the screenshots below you can the warped image with the vector field of the registration and the fixed and moving image. 
Do you have a suggestion to remove the holes?

Thank you!

Kind regards, 
Franciska 
Registration.PNGImages.PNG

Op donderdag 24 augustus 2023 om 17:15:59 UTC+2 schreef lena....@gmail.com:
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