[Elastix] Memory issue with Rigid+BSpline Transform

Vogler, Steffen /DZNE Steffen.Vogler at dzne.de
Mon Feb 23 15:39:23 CET 2015


Dear Elastix-Community,

I am a new user of Elastix interested in registration of single 2D section to 3D microCT reference. Since the dimensions have to match I converted the 2D-image into a 3D stack (z=1) beforehand. I would like to do a rough registration (rigid) first, followed by an exact second registration (BSpline) step. Both steps work fine, when executed separately but I run into a memory issue when I doing both registrations back-to-back. Specifically, I ran into a core dump while computing JacobianTerms in the BSpline transform. In my current dummy-example, however, both images are smaller than 8MB while RAM is as big as 32GB.
Could you please point out what I am doing wrong? I thought Rigid+BSpline registration should be quite a standard job to do. Any help is highly appreciated.

This is the command used:
elastix -m input/canon_T1_r.mha -f input/slice555_deform.mha -p Parameters_Rigid.txt -p Parameters_BSpline.txt -out ./output_Rigid+BSpline/

Here are the two images used:
https://www.dropbox.com/s/v8y17ko3q0mfb8o/canon_T1_r.mha?dl=0
https://www.dropbox.com/s/i89jbjims9nlhig/slice555_deform.mha?dl=0

Here are the two parameter files used:
https://www.dropbox.com/s/n5wnsyhg298vtlq/Parameters_Rigid.txt?dl=0
https://www.dropbox.com/s/y5ypxbphahl8ziu/Parameters_BSpline.txt?dl=0

Kind regards,
Steffen


**********************

Steffen Vogler
Predoc (Group Kempermann)
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
Partnerstandort Dresden
Arnoldstraße 18 / 18b
01307 Dresden

t- +49 (0) 351 210 463 19
web   http://www.dzne.de

***********************

Executive Board: Prof. Pierluigi Nicotera, MD PhD (Chairman of the Executive Board and Scientific Member of the Executive Board) and Dr. Sabine Helling-Moegen, LL.M. (Administrative Member of the Executive Board)
The DZNE is registered in the association register of the Bonn District Court (Amtsgericht Bonn) (Az. VR 9021).

***********************


More information about the Elastix mailing list