Hi there, I have 2 image sets: one is a high resolution CT from a small specimen with 0.15, 0.15, 0.15 millimeter spacing in each of the X, Y and Z axis, the other one is an optical stack of the same specimen taken using a digital camera with the following spacing (mm) in x,y,and z axis respect…

Hi Andras, I tried the latest version and also tried not to center the images this time, and it worked (previously the images were centered before registration). So I got good alignments when I set the fixed and moving image as follows: Fixed image: optical (0.05, 0.05, 3 millimeter spacing) M…

[image] Niousha_Aflatouni: tried not to center the images Never center images if you need proper alignment. If centering is enabled then it forces Slicer to ignore image origin information that is stored in the image header. [image] Niousha_Aflatouni: to do the reverse registration Sl…

Hi Andras, I tried the inverse transform the way you explained and I can see the change in the image but I still have the same issue as before: the hardened image can not be saved and the same error message appears. I couldn’t figure out what the issue is. Any thoughts on that? As for the inten…

[image] Niousha_Aflatouni: the hardened image can not be saved Saving should be no problem, but maybe if it’s a color image there may be issues. Could you try if saving works if you convert the image to scalar (grayscale) volume (using Vector to scalar volume module)? [image] Niousha_Afl…

Hi Andras, Thanks for the info. After many trials, I realized that the images should be cropped and turned into gray scale both in 3D Slicer, and if those are initially done in MATLAB then they won’t work in 3D Slicer. I also found a feature in 3D Slicer called Metric Test, that seems to enable…

[image] Niousha_Aflatouni: if those are initially done in MATLAB then they won’t work in 3D Slicer What do you mean? What do you expect to happen and what happens?

[image] Niousha_Aflatouni: There was however no documentation for this feature that I could find I think the only help is in the tooltips. Let us know if anything is unclear. [image] Niousha_Aflatouni: I was wondering is this something that I can reliably use for calculating the MI Y…

Hi Andras, Thanks for your previous answers. I had some questions about the Metric Test to calculate MI; I’m interested in obtaining the MI value of a specific region from the images rather than the entire image sets. I understand that this normally can be done using Masking but I couldn’t find …

You have two options: Option A: Extend the Metric Test module to accept mask images. You need to build Slicer from source code and be somewhat familiar with C++ programming (so that you can find out where to add the masking option). Option B: Create a simple scripted module that computes the metri…

Hi Andras, Can you provide some instructions on how to access the source code? I followed the instructions provided in here: https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions#CHECKOUT_slicer_source_files but it wasn’t clear to me what should be done next and how to …

CT to optical image registration

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CT to optical image registration

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