Specify name for output file in elastix/transformix

[Rose]

Hi, 

I'm using elastix in MATLAB to register multiple sets of images. I first perform the registration on one type of image, then I apply the resulting transformation to another three types of image. The output is always called essentially the same thing, some variation on "result.mhd". It would be convenient if I could save it under a different name, so as to not get the different image types mixed up, or at least rename it afterwards (but I view the results in Slicer, which does not seem to like it when mhd files have been renamed?). 

I've seen that this feature exists in SuperElastix (https://github.com/SuperElastix/elastix/issues/672), but as I use elastix from within MATLAB I wondered if there are any plans to implement this, or whether there already is a way that I'm unaware of?

Any thoughts would be much appreciated!

Thanks,

Rose

[Konstantinos Ntatsis]

Hi Rose,

All elastix functionality is written in C++ and, as you correctly pointed out, can be found in the following repo: https://github.com/SuperElastix/elastix. In addition to C++, elastix can be used via the python ITK wrapper (https://github.com/InsightSoftwareConsortium/ITKElastix) or for quite a few additional languages via the SimpleITK wrapper (https://simpleitk.readthedocs.io/en/master/about.html). Since MATLAB is not part of these two official wrappers, I am assuming that you are using another wrapper developed from some member(s) of the community.

I think the best would be to ask directly the maintainers of the MATLAB wrapper that you are using if they could update to the latest Elastix version (https://github.com/SuperElastix/elastix/releases/tag/5.1.0) since the functionality is already there (ie. no need to implement something specifically for MATLAB). Let me know if that helps.

Kind regards,

Konstantinos

[m.st...@lumc.nl]

If I am not mistaken, you can use python within matlab nowadays.

Best, Marius

---

From: elastix-imag...@googlegroups.com <elastix-imag...@googlegroups.com> on behalf of Konstantinos Ntatsis <konstantino...@gmail.com>
Sent: 13 March 2023 10:48 AM
To: elastix-imageregistration
Subject: [elastix-imageregistration] Re: Specify name for output file in elastix/transformix

 

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[Tom Birdsong]

Hi all,

Adding on here, we recently published an Insight Toolkit blog post detailing how to use ITK Python packages in MATLAB for image processing. The same mechanics will likely allow up-to-date versions of the ITKElastix Python wrapper to be used in MATLAB. Please see https://www.kitware.com/leverage-the-powerful-insight-toolkit-itk-in-matlab-via-python/

Best,

Tom

[mfk16]

Hi Rose,

What MATLAB wrapper are you using? I use a matlab wrapper and it's possible to change the output name.

Thanks,

Matt