[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:

Here are the two parameter files used:

Kind regards,


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

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