PET processing

[atwu]

To whom it may concern,

Hello! I downloaded the PET scans, but when I can't seem to find a NIFTI file/volumetric file. I've tried downloading through the PUP and through the normal download_scans method, but for PUP I only found T1 and wmparc nifti volumes and through downloading normal_scans the nifti file in each folder looks like noise. Is there something I am doing wrong/additional processing that I need to do? If so, can you direct me to the appropriate resources to process them? Thanks!

[sarahkeefe]

Hi, This depends on what you are looking for. The PET session NIFTIs are unprocessed and will look somewhat noisy (but brain-shaped as you scroll through them). Those would be downloaded with the scan download scripts (download_scans/download_oasis_scans.sh, etc). That would be what you want if you are going to perform your own PET processing on unprocessed NIFTI-formatted PET scan files.

The PUP processing output provided with OASIS3 and OASIS4 contains a number of processed image outputs. That includes SUVR images: the *n_msum_SUVR.nii which is unsmoothed and *n_msum_SUVR_g8 which has been smoothed. These SUVR images were calculated with the FreeSurfer Cerebellum-Cortex region as the reference region. PUP processing was performed on PET scans that had an associated MR scan that took place within 1 year of PET and that MR scan passed our internal FreeSurfer QC. Those processed PET images can be downloaded as part of PUP processing (download_pup/download_oasis_pup.sh).

I hope this helps! I will keep this issue open for a little bit in case you have follow-up questions.