Starting with PET volume pipeline

[Enrique Franky]

Hi everyone,

I am currently exploring the Clinica software because I want to perform SPM analysis on PET images. I am a bit confused about whether the 't1-volume – Volume-based processing of T1-weighted MR images with SPM prerequisite' requires MRI images to be taken alongside the PET data. I apologize if this is just a misunderstanding on my part, but I am unsure if the PET dataset needs to include MRI images for this step.

[ninon....@gmail.com]

Hello Enrique,

To process PET images you indeed need corresponding T1w MR images. More specifically, you need to have both for each subject/session. Your BIDS directory should look like that:

BIDS_Dataset/
├── sub-CLNC01/
│   │   ├── ses-M00/
│   │   │   ├── anat/
│   │   │   │   ├── sub-CLNC01_ses-M00_T1w.json
│   │   │   │   └── sub-CLNC01_ses-M00_T1w.nii.gz
│   │   │   ├── pet/
│   │   │   │   ├── sub-CLNC01_ses-M00_trc-18FFDG_pet.json
│   │   │   │   ├── sub-CLNC01_ses-M00_trc-18FFDG_pet.nii.gz
│   │   │   └── sub-CLNC01_ses-M00_scans.tsv
│   │   ├── ses-M18/
│   │   │   └── ...
│   │   └── sub-CLNC01_sessions.tsv
├── sub-CLNC02/
│   └── ...
├── ...

└── participants.tsv

Hope this helps.

Best,
Ninon

[Enrique Franky]

Hi Ninon,

I just spoke with the team responsible for collecting the PET image dataset, and I acknowledge that the anatomical reference is based on CT rather than MRI. Is it still possible to proceed with Clinica for the SPM processing, or does this eliminate the option of using it as our platform?

[ninon....@gmail.com]

Hi Enrique,

I'm afraid you won't be able to use Clinica to process your PET images then. You could still use SPM though. In this case, you need a PET template to spatially align your images (e.g. the Dementia-Specific [18F]-FDG-PET template). I'm not very familiar with this processing but there should be some guidelines (here for example).

Best,

Ninon