[Elastix] TR: Question about registration of three different modalities.

Fabien PERTUY pertuy at igbmc.fr
Tue Nov 10 12:23:51 CET 2015


Sorry, forgot to cc the mailing list.

De : Fabien PERTUY
Envoyé : mardi 10 novembre 2015 12:22
À : 'ibraheem aldhamari' <ibr_ex at yahoo.com>
Objet : RE: [Elastix] Question about registration of three different modalities.

Hi Ibraheem,

Maybe you can try what is indicated here: http://elastix.isi.uu.nl/FAQ.php#Q_TooManySamples

You can try translation transform using (Transform "TranslationTransform") instead of EulerTransform (Rigid)

Fabien

De : ibraheem aldhamari [mailto:ibr_ex at yahoo.com]
Envoyé : mardi 10 novembre 2015 11:48
À : Fabien PERTUY <pertuy at igbmc.fr<mailto:pertuy at igbmc.fr>>; elastix at bigr.nl<mailto:elastix at bigr.nl>
Objet : Re: [Elastix] Question about registration of three different modalities.

Hi Fabien,
 thanks for your quick reply and useful tips. I tried both way: - img3 as moving and transformed img2 as fixed. - img1 as moving and transformed img2 as fixed. The result either bad registration or an error:   "Too many samples map outside moving image buffer"
I activated the testing and rebuild elastix again and found the binary elxInvertTransform but after I ran the program nothing happened, no error message or output (I used only Rigid transform for just testing if I can get back to the original image).
After doing landmarks registration using 3D Slicer, I found out that I need only a translation transform. Is there anyway to enhance the registration using Translation transform by changing specific parameters?
Here is more information about the images:
img1, CT_hr: Part of head, Size( 503,503,167), Spacing( 0.16mm, 0.16mm, 0.48mm), Origin(40.2mm, 40.2, -39.8mm), Directions [ -1,0,0;0,-1,0; 0,0,1],  MinMax( -32651, 32607), Data_type(short).  img2 CT_lr: Head, Size( 512,512,50), Spacing( 0.40mm, 0.40mm, 1mm), Origin(96.7mm, 283.7,-427mm), Directions [ -1,0,0;0,-1,0; 0,0,1],  MinMax( -1024,2806),Data_type(short).  img3 MR: Head, Size(384,512,64), Spacing( 0.39mm, 0.39mm, 0.7mm), Origin(80.8mm, 116.1mm, -56.1mm), Directions [ -1,0,-0.0018;-0.0004,-0.9794,0.2020; -0.0018,0.2020,0.9794],  MinMax( 0, 2963),Data_type(unsigned short).
  Best regards and have a nice day!
  Ibraheem


________________________________
From: Fabien PERTUY <pertuy at igbmc.fr<mailto:pertuy at igbmc.fr>>
To: ibraheem aldhamari <ibr_ex at yahoo.com<mailto:ibr_ex at yahoo.com>>; "elastix at bigr.nl<mailto:elastix at bigr.nl>" <elastix at bigr.nl<mailto:elastix at bigr.nl>>
Sent: Monday, November 9, 2015 11:30 PM
Subject: RE: [Elastix] Question about registration of three different modalities.

Hi Ibraheem,

Can't you register img3 as moving with the transformed img2 as fixed ?

Otherwise maybe you should provide more info about the images (modalities, etc...)

You can activate inverse transform when configuring CMake before building the project.

Hopes it will help,

Best,

Fabien
________________________________
De : ibraheem aldhamari<mailto:ibr_ex at yahoo.com>
Envoyé : ‎09/‎11/‎2015 18:00
À : elastix at bigr.nl<mailto:elastix at bigr.nl>
Objet : [Elastix] Question about registration of three different modalities.

Hi,
I have three types of images (img1, img2 and img3) from different moralities. I need to register them all.  After I tried many options, I finally can register img1 as a fixed image and img2 as a moving image, I also can register img3 as fixed image and img2 as a moving image but I can not register successfully img1 and img3. Is it possible to use the results I have to register img1 and img3?
I thought about using the inverse transform as written in the manual but it does not work (or maybe I used it wrong). Also, after I built elastix from the source I can not find a binary file for elxInvertTransform.

Best regards and have a nice day!
Ibraheem


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