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Daniel Markel

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10 Feb 2012 Screenshot 3D Free Form Image Registration Toolbox (GUI) A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. Author: Daniel Markel geometric transformat..., image registration, 3d, registration, image, free form 64 14
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4.0 | 2 ratings
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20 Jun 2014 Extract Slice from Volume ExtractSlice extracts an arbitrary slice, both intensities and indices, from a given volume. Author: ted p teng

I found an error when using this in 2013a occasionally when rotating the plane it would give me coordinates outside of the volume and thus return NaNs. I found changing line 95 to

rotate(hsp,hspVecXvec(:)',180*acosineVal/pi,[0,0,0]);

fixes the problem by specifying the origin when rotating.

Cheers,

-Daniel

21 May 2009 3D Free Form Image Registration Toolbox (GUI) A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. Author: Daniel Markel

Sorry the first part of the comment was cut off.

The label can be anything you want, it's just what the program will call the data set after you load it in. All I recommend is not using the words 'temp' or 'deform' in the title.

Put the data files into any folder on your computer, you'll be able asked to select it once you're adding an image dataset. I wouldn't mess around with the 'patient files' folder. the program will manage it on it's own.

I should add, there's a bit of an order to using the GUI, I apologize there's no manual yet.

1. 'create new patient' or load an exisiting one first.
2. Now you can add images to you're patients file it's expected that they are 3D volumes and all images pertaining to it are in the same folder.
3. Once the data is in the program you can select it in the list and click 'View data' to see it or you can select 'load contours' to load in any ROI's that accompanied the data set, they should also be in the dicom or RTOG files (this is optional).
4. Click 'Feature points' to mark any fudicials between data sets. The points are colour coded on the screen to correspond to the first or second image. The fade slider goes from 'image1 ---> image2'. (This is also optional)
5. In the pull down menu in the main program you can select 'Registration Parameters' to change the optimization parameters to get a better or faster registration.
5. Click register points to set up a single or series or registrations. If there are no contours you can select 'auto segment' in the registration menu to have the program use thresholding to segment the images. Once you're ready hit 'Register' and leave the program until it's finished, this may take a while.
6. Once done, the registration parameters will appear in the 'Deform' menu (purple button). You select the data set you're applying the transformation to on the left and the transformation on the right. Hit 'Apply deformation' to produce a data set of the deformed volume (remember you can only output in dicom for now). 'Load dose' to load a dose volume to accompany the data set. Or 'Calculate DVH' to apply the transformation to a dose set and produce an excel file with the DVH data.

21 May 2009 3D Free Form Image Registration Toolbox (GUI) A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. Author: Daniel Markel

P.S. or if you're loading an RTOG you would select the header file within that folder.

Cheers,

-Dan

11 May 2009 3D Free Form Image Registration Toolbox (GUI) A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. Author: Daniel Markel

Sorry for the delay, that's not a bad idea. Here's an RTOG of a phantom, you have to unzip it first, first file 0%0000 is the header. I have gotten rid of almost all the bugs now, I'll try to upload the fixed version tommorrow.

http://rapidshare.com/files/231809097/example.zip

Comments and Ratings on Daniel Markel's Files View all
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28 Mar 2014 3D Free Form Image Registration Toolbox (GUI) A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. Author: Daniel Markel Nicolas Yu

No mannual. And the directories are better to be relative directories.

29 Jul 2012 3D Free Form Image Registration Toolbox (GUI) A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. Author: Daniel Markel ava

Thanks for the code,
How is it possible to test the software for 3D Mesh model?

Thanks again

27 Oct 2011 3D Free Form Image Registration Toolbox (GUI) A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. Author: Daniel Markel Tsenmu

16 Aug 2011 3D Free Form Image Registration Toolbox (GUI) A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. Author: Daniel Markel amin moham

thanks for toolbox
can i use your functions for 2d image registration(motion maping in video)?

11 Jul 2011 3D Free Form Image Registration Toolbox (GUI) A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. Author: Daniel Markel Eman Alsayyad

can i use this free form deformation code to deform a human body template model to an individual human by having 2 contour images one for the template and the other for the target if yes ,which files or functions can i use if no ,have you any background about how i can do that?
please reply as soon as possible it is an important issue thank you

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