BrainVISA

Hi, I finally solved the problem of the meshes, the problems was that the ITK world is almost the scanner-based anatomical referential, because, as I showed before, there is additionally a flipping of both the X and Y axes. So, finally, to convert from Aims to ITK space we need first to to apply the...

Hi Denis, I agree that there are two different problems: 1) Probably BrainVisa Morpohologist pipeline doesn't save the brain segmentations (left cortex, right cortext etc) in the same reference frame as the original image (while the brain mask for example is in the same reference) 2) The mesh are sa...

Hi, The problem is not only related to MITK, the exact same thing would happen also using MedInria. Additionally, I do not understand why in the Morphologist pipeline the brain mask is registered to the image, but for example the segmented cortex not (see attachment). What is the trasformation appli...

I spoke too fast.. The mesh and the image looked well aligned but indeed they are not perfectly registered. Does the AC-CP transformation play any role in this issue? I attach my script and what I get. I have a last step in which I conver ply to VTK with Paraview but I believe and hope that the prob...

Yes, Perfect! I was close to the solution indeed
Thanks a lot for your quick help!

Hello, I am using a simple Python script to save into a single mesh file the meshes extracted from the sulci graph generated by the Morphologist pipeline. This works perfectly and in Anatomist I can see the MRI with the extracted mesh perfectly registered. However using other programs (like MITK) th...