Operating system: Mac OSX 10.9.5 Slicer version: 4.7 I am trying to run a registration in the BRAINS module, that is somewhat unique and different from the sample cases given online. I have a grayscale FA scalar volume image file (obtained from a DTI volume file), and I have generated an FEM mask …

[image] Rewati_Kulkarni: Changing the visibility of the files does not help at all. I am able to only see the file I load last, whichever it may be This is because the two volumes don’t overlap at all (this confirms that the “Joint PDF summed to zero” error is due to non-overlapping contours)…

[image] Rewati_Kulkarni: Joint PDF summed to zero This error typically occurs when the fixed and moving images do not overlap. Either translate them manually to be approximately in the same position and harden the transform; or try one of the automatic initial alignment options.

Is that why I’m unable to view both images when I load them? because they do not overlap? However, as mentioned in my post, I ensured that both their centers were situated at 0,0,0. Shouldn’t this be solving the problem? Rewati Kulkarni Research Assistant, Injury Biomechanics Lab. University o…

Choose one image in the red slice viewer, the other in the green slice viewer, and on both of them reset the field of view and show it in 3D (click the small rectangle and the eye icon in the slice view controller, complete the basic 3D Slicer tutorials if you are not sure how to do these). Then you…

[image] Rewati_Kulkarni: I ensured that both their centers were situated at 0,0,0. Shouldn’t this be solving the problem? You mentioned that some of your data is generated some Matlab code. It is quite possible that the results you saved from that code lose the direction/spacing information …

I would recommend to use nrrdread.m and nrrdwrite.m functions (available in the MatlabBridge extension or can be downloaded from here ). These are well tested and set preserve origin, spacing, and directions information properly. By the way, why don’t you use the MatlabBridge extension for running …

Thank you for all your responses! I was able to fix the issue and get the registration working.

General registration (BRAINS) returns "Joint PDF summed to zero" error

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General registration (BRAINS) returns "Joint PDF summed to zero" error

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