Command line execution of ITK-SNAP registration?

[j.cos...@jatneurolab.com]

Does anyone know if there is a command-line way to execute the ITK-SNAP registration (e.g., c3d)? For a certain dataset, repeatedly, the registrations I obtain from ITK-SNAP are better than the FSL recipe I created.

Either way, nice job on the registration routine developer!

- Jamie

[Paul Yushkevich]

Thanks!

Yes, the registration is available in standalone form, also includes deformable registration:

https://sites.google.com/view/greedyreg/about

Paul

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[Jamie Costabile]

I installed 'greedy' received roughly 10 warnings and no errors. But when I run the command:

greedy -d 3 -i ../../T1ns.nii b0ns.nii -o tmp.nii -a -m MI -threads 8

The tmp.nii file fails to open. Any ideas?

On Tue, Aug 21, 2018 at 7:46 AM, Paul Yushkevich <pyush...@gmail.com> wrote:

Thanks!

Yes, the registration is available in standalone form, also includes deformable registration:

https://sites.google.com/view/greedyreg/about

Paul

On Mon, Aug 20, 2018 at 8:38 PM <j.cos...@jatneurolab.com> wrote:

Does anyone know if there is a command-line way to execute the ITK-SNAP registration (e.g., c3d)? For a certain dataset, repeatedly, the registrations I obtain from ITK-SNAP are better than the FSL recipe I created.

Either way, nice job on the registration routine developer!

- Jamie

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

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[Paul Yushkevich]

Jamie,

With -a you are selecting affine registration. The output should be a matrix file (.mat). You will need to run a second command to apply that matrix to the input image to reslice it into the fixed image space. 

Please see 'my first registration' here: https://sites.google.com/view/greedyreg/quick-start?authuser=0

Paul

On Tue, Aug 21, 2018 at 2:16 PM Jamie Costabile <j.cos...@jatneurolab.com> wrote:

I installed 'greedy' received roughly 10 warnings and no errors. But when I run the command:

greedy -d 3 -i ../../T1ns.nii b0ns.nii -o tmp.nii -a -m MI -threads 8

The tmp.nii file fails to open. Any ideas?

On Tue, Aug 21, 2018 at 7:46 AM, Paul Yushkevich <pyush...@gmail.com> wrote:

Thanks!

Yes, the registration is available in standalone form, also includes deformable registration:

https://sites.google.com/view/greedyreg/about

Paul

On Mon, Aug 20, 2018 at 8:38 PM <j.cos...@jatneurolab.com> wrote:

Does anyone know if there is a command-line way to execute the ITK-SNAP registration (e.g., c3d)? For a certain dataset, repeatedly, the registrations I obtain from ITK-SNAP are better than the FSL recipe I created.

Either way, nice job on the registration routine developer!

- Jamie

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

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[Jamie Costabile]

Ahh, thank you! I'll work through the example.

On Tue, Aug 21, 2018 at 12:18 PM, Paul Yushkevich <pyush...@gmail.com> wrote:

Jamie,

With -a you are selecting affine registration. The output should be a matrix file (.mat). You will need to run a second command to apply that matrix to the input image to reslice it into the fixed image space. 

Please see 'my first registration' here: https://sites.google.com/view/greedyreg/quick-start?authuser=0

Paul

On Tue, Aug 21, 2018 at 2:16 PM Jamie Costabile <j.cos...@jatneurolab.com> wrote:

I installed 'greedy' received roughly 10 warnings and no errors. But when I run the command:

greedy -d 3 -i ../../T1ns.nii b0ns.nii -o tmp.nii -a -m MI -threads 8

The tmp.nii file fails to open. Any ideas?

On Tue, Aug 21, 2018 at 7:46 AM, Paul Yushkevich <pyush...@gmail.com> wrote:

Thanks!

Yes, the registration is available in standalone form, also includes deformable registration:

https://sites.google.com/view/greedyreg/about

Paul

On Mon, Aug 20, 2018 at 8:38 PM <j.cos...@jatneurolab.com> wrote:

Does anyone know if there is a command-line way to execute the ITK-SNAP registration (e.g., c3d)? For a certain dataset, repeatedly, the registrations I obtain from ITK-SNAP are better than the FSL recipe I created.

Either way, nice job on the registration routine developer!

- Jamie

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

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[Jamie Costabile]

Thank you, Paul, great work!

Two questions for you about 'greedy': (1) Is it possible to execute rigid body registrations with this? (2) Do you have an opinion on executing deformable registrations on diffusion tensor images?

- Jamie

[Jamie Costabile]

I found the first answer top the first question, which is yes. How do I execute the rigid body registration?

[Jamie Costabile]

Excuse me, I found the answer to (1) in the Documentation on the website. However, I perused the -help list beforehand without seeing the '-dof' input option.

[Karan Jeswani]

I really want to use the command line version for registration as I want to do the same for 100s of image-pairs.

I am having problems installing greedy.

I am following https://sites.google.com/view/greedyreg/installation, its asking me the directory in which I compiled itk! This I don't have.

Will I have to build itksnap from source?

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

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[Paul Yushkevich]

You can just install itksnap and run Help->Install Command-Line Tools to get greedy installed.

Paul

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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

[Michael Martin]

As per your message here as well as at https://sites.google.com/view/greedyreg/installation, I've installed ITK-SNAP 3.8, launched it, but my help tab just has "About ITK-SNAP", "Check for Software Updates ... ", and "Documentation Home ...". Am I in the wrong help tab? Would very much appreciate any help as I am trying to install greedy and haven't been able to successfully compile from the source code. 

Michael

[Paul Yushkevich]

Hi Michael,

I recently made greedy binaries available directly on SourceForge:

https://sourceforge.net/projects/greedy-reg/files/Experimental/

Thanks,

Paul

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[Michael Martin]

Marvelous, thank you very much!