change of default filled HU value of the img_out in rigid registration

[Sheng Joey]

Dear all,

I have used the "registor" to registrate two CT images and output the new CT image.

It worked quite well. 

However, the boundary of the generated image was filled by HU value of 0. Which in my case I would fill it with HU -1000. See the attached figure and the code. How could I change the default fill values?

Thanks.

Best regards,

Joey

Here is the code:

# command_file.txt

[GLOBAL]
fixed=CTori.nrrd
moving=CTnew.nrrd
fixed_roi=body.nrrd
img_out=warped_6d_mask_trip.nrrd

[STAGE]
xform=align_center
[STAGE]
xform=translation
optim=amoeba
[STAGE]
xform=rigid
max_its=50
res=4 4 2

[Sharp, Gregory C.,PHD]

Hi Joey,

The best way to do this is to use two steps.

First, run the register command and create a transform. For rigid, it is something like:
xform_out=rigid.tfm

For deformable, it could be:
xform_out=vf.mha

These would go in the GLOBAL section or in the last stage.

Then the second step, use the transform to warp the image.

plastimatch warp --default-value -1000 --input image.mha --output registered.mha --xf rigid.tfm (or --xf vf.mha)

Greg

________________________________________
From: plast...@googlegroups.com <plast...@googlegroups.com> on behalf of Sheng Joey <18157...@gmail.com>
Sent: Wednesday, October 5, 2022 5:37 PM
To: Plastimatch
Subject: [Plastimatch] change of default filled HU value of the img_out in rigid registration

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Dear all,
I have used the "registor" to registrate two CT images and output the new CT image.
It worked quite well.
However, the boundary of the generated image was filled by HU value of 0. Which in my case I would fill it with HU -1000. See the attached figure and the code. How could I change the default fill values?
Thanks.

Best regards,
Joey

[fillwith-1000insteadof0.png]

Here is the code:

# command_file.txt

[GLOBAL]
fixed=CTori.nrrd
moving=CTnew.nrrd
fixed_roi=body.nrrd
img_out=warped_6d_mask_trip.nrrd

[STAGE]
xform=align_center
[STAGE]
xform=translation
optim=amoeba
[STAGE]
xform=rigid
max_its=50
res=4 4 2

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[Sheng Joey]

Dear Greg,

Thank you for your quick reply.

The following command worked just as expected.

>plastimatch warp --default-value -1000 --input  CTnew .nrrd --output-img wrapoutfile.nrrd --xf rigid_xf.tfm

Thank you very much.

Best regards,

Joey