PET-CT and skull-strip

Hello everyone,

I’m looking to perform a VBM (Voxel-Based Morphometry) analysis using the SPM (Statistical Parametric Mapping) algorithm implemented in Jupyter notebooks (Collab) with FDG PET images. However, the data I have uses CT scans as the anatomical reference, which has left me a bit confused since most examples and tutorials I’ve found are based on MRI data. I’m wondering if there’s a way to wrap into an atlas from the CT reference images or even use them to generate the atlas? Additionally, is it possible to coregister the CT scans with the PET images to facilitate the VBM analysis with SPM? Any help on this matter would be greatly appreciated. Also, I haven’t found another platform that implements the SPM workflow as effectively as I intend to use the Clinica software here.

Moreover, my search on OpenNeuro yielded no FDG PET/CT databases. Therefore, I am actively seeking alternative repositories that might contain such datasets. If you’re aware of any, please share them with me. Your assistance would be greatly appreciated.

Thank you in advance for any assistance you can provide.

The Clinical Toolbox for SPM can normalize CT scans. I would thing you could coregister the PET emission scans to the CT transmission scan, normalize the CT and apply the CT transform to the PET scan. Not sure if it is possible to do anything like this with Jupyter, but I would think it would work with Octave.

If you REALLY want to stay in the world of jupyter notebook, there is an octave kernel for jupyter notebooks: I have used it here and there (link)

would require:

problem is that I am not sure that all SPM toolboxes (like the one mentioned above) is tested with octave.