[Elastix] Question about registration of three different modalities.

ibraheem aldhamari ibr_ex at yahoo.com
Tue Nov 10 15:17:40 CET 2015


Hi Fabien,
The link was helpful, thanks. I added (RequiredRatioOfValidSamples 0.01) and no error anymore but still the registration is not good.I already tried these transforms and different combinations of two or three of them: Translation, Euler, Affine and PSpline but so far no luck in getting good registration.  Any other Suggestion? Best regards and have a nice day!Ibraheem   

     From: Fabien PERTUY <pertuy at igbmc.fr>
 To: ibraheem aldhamari <ibr_ex at yahoo.com> 
 Sent: Tuesday, November 10, 2015 12:22 PM
 Subject: RE: [Elastix] Question about registration of three different modalities.
   
#yiv8726020808 -- filtered {font-family:Helvetica;panose-1:2 11 6 4 2 2 2 2 2 4;}#yiv8726020808 filtered {panose-1:2 4 5 3 5 4 6 3 2 4;}#yiv8726020808 filtered {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}#yiv8726020808 p.yiv8726020808MsoNormal, #yiv8726020808 li.yiv8726020808MsoNormal, #yiv8726020808 div.yiv8726020808MsoNormal {margin:0cm;margin-bottom:.0001pt;font-size:12.0pt;}#yiv8726020808 a:link, #yiv8726020808 span.yiv8726020808MsoHyperlink {color:blue;text-decoration:underline;}#yiv8726020808 a:visited, #yiv8726020808 span.yiv8726020808MsoHyperlinkFollowed {color:purple;text-decoration:underline;}#yiv8726020808 span.yiv8726020808EmailStyle17 {color:#1F497D;}#yiv8726020808 .yiv8726020808MsoChpDefault {font-size:10.0pt;}#yiv8726020808 filtered {margin:70.85pt 70.85pt 70.85pt 70.85pt;}#yiv8726020808 div.yiv8726020808WordSection1 {}#yiv8726020808 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>; 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>
To: ibraheem aldhamari <ibr_ex at yahoo.com>; "elastix at bigr.nl" <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
Envoyé :‎09/‎11/‎2015 18:00
À :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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