Working document for PET processing.
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Gaele, 30th AUgust 2023
Working with the nifti files converted in MRIcroGL
I extracted the bone part of the MRI template or kept only the soft tissue. I did that by using the corresponding Atlas, binary masked. It worked well
I segmented the CT to keep only the intensities corresponding to the bone, so basically I got rid of the noise.
I put the segmented CT in the same "space" as the template coronal-coronal, axial-axial, sagittal-sagittal, manually
I run Coregistration estimate, and that is the result in the file attached. the best results were obtained with the Template where the brain was segmented, without skull, nor tissue around and, with the segmented skull. Interestingly enough the template without brain, with skull and tissue didn't work very well.
The next step is to do the "warping" or scaling (affine transformations)
-->can I use the reslice estimate option allowing for warping in x, y, z or you showed me another option with old normalise,...but I couldn't remember where that was.
The reslice option does not scale.
-->also, do you suggest me to use the output of step 4 to do the last step with scaling or to use the affine transformation at once?
