brainstorm3 icon indicating copy to clipboard operation
brainstorm3 copied to clipboard

Add PET volume processing: SUVR, ROI masking, projection to surface, SPM-petpve plugin

Open DiellorBasha opened this issue 7 months ago • 1 comments

PET processing functionalities, extending the previously integrated PET import pipeline.

Features:

  • Atlas-based ROI masking, using existing '_volatlas' files in Brainstorm
  • Intensity rescaling (SUVR)
  • Volume-to-surface projection
  • GUI/dialog for collecting user input for PET processing
  • PETPVE plugin as an SPM toolbox

New functions:

  • process_pet.m: scriptable entry point for PET processing - used to chain together PET processing functions
  • panel_process_pet.m: GUI for collecting user input for PET processing - works with process_pet.m
  • mri_rescale.m: rescale intensity values (e.g. SUV/SUVR) using the mean value of a reference regions - works with panel_process_pet.m and mri_mask.m
  • mri_mask.m: bilateral ROI-based volume masking using atlas labels from supported atlases: "aseg", "Desikan-Killiany" and so on.
  • mri_interp_vol2tess.m: interpolates 3D PET volumes onto cortical surfaces

Please let me know if further modularization or code cleanup is needed. Thanks for reviewing!

DiellorBasha avatar May 22 '25 10:05 DiellorBasha

Ping @DiellorBasha

rcassani avatar Jun 16 '25 18:06 rcassani

Thank for the review @rcassani and apologies for the delay. I've made the requested changes - see e10d74789b0e05dd1abf3617273fd0ea8c305ea5

DiellorBasha avatar Jun 26 '25 06:06 DiellorBasha

@DiellorBasha, the code PR is good to be merged. The documentation is missing. Please complete: https://neuroimage.usc.edu/brainstorm/Tutorials/PetProcessing

After that we can merged to master

rcassani avatar Jul 04 '25 18:07 rcassani