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Clinica & BIDS specifications for PET modality

Since Clinica v0.6, PET data following the official specifications in BIDS version 1.6.0 are now compatible with Clinica. See BIDS page for more information.

Partial volume correction (PVC)

To correct for partial volume effects, several PVC algorithms exist and are implemented in the PETPVC toolbox.

To perform PVC (compulsory for pet-surface, optional for pet-volume), you will need to specify in a TSV file the full width at half maximum (FWHM), in millimeters, of the point spread function (PSF) associated with your data, in the x, y and z directions.

For instance, if the FWHM of the PSF associated with your first image is 5 mm along the x and y axes, and 6 mm along the z axis, the first row of your TSV file will look like this:

participant_id    session_id     acq_label     psf_x    psf_y    psf_z
sub-CLNC0001      ses-M00        18FFDG        5        5        6
sub-CLNC0001      ses-M00        18FAV45       4.5      4.5      5
sub-CLNC0002      ses-M00        18FFDG        5        5        6
sub-CLNC0003      ses-M00        18FFDG        7        7        7

Since the PSF depends on the PET tracer and scanner, the participant_id, session_id, acq_label, psf_x, psf_y and psf_z columns are compulsory.

The values in the column acq_label should match the value associated to the trc key in the BIDS dataset. For example in the following BIDS layout the values associated would be 18FFDG and 18FAV45:

└─ sub-CLNC0001
   └─ ses-M00
      ├─ sub-CLNC001_ses-M00_trc-18FAV45_pet.nii.gz
      └─ sub-CLNC001_ses-M00_trc-18FFDG_pet.nii.gz

Reference regions used for intensity normalization

In neurology, an approach widely used to allow inter- and intra-subject comparison of PET images is to compute standardized uptake value ratio (SUVR) maps. The images are intensity normalized by dividing each voxel of the image by the average uptake in a reference region. This region is chosen according to the tracer and disease studied as it must be unaffected by the disease.

Clinica v0.3.8 introduces the possibility for the user to select the reference region for the SUVR map computation.

Reference regions provided by Clinica come from the Pick atlas in MNI space and currently are:

  • pons: 6 mm eroded version of the pons region

  • cerebellumPons: 6 mm eroded version of the cerebellum + pons regions

  • pons2: new in Clinica v0.4

  • cerebellumPons2: new in Clinica v0.4

In Clinica v0.4 two new versions of these masks have been introduced: pons2 and cerebellumPons2. Indeed we wanted to improve the reference regions mask to better fit the MNI152NLin2009cSym template used in linear processing pipelines. The new masks still come from the Pick atlas but with a different processing: we decided to first truncate the mask using SPM12 tissue probability maps to remove voxels overlapping with regions outside the brain (bone, CSF, background...). Then, we eroded the mask using scipy binary_erosion with 3 iterations.

Tutorial: How to add new SUVR reference regions to Clinica?

It is possible to run the pet-surface and pet-volume pipelines using a custom reference region.

  • Install Clinica following the developer instructions ;

  • In the <clinica>/clinica/utils/ file, modify the following two elements:

    • The label of the SUVR reference region that will be stored in CAPS filename(s):

    Simply define a new label that will be your new SUVR reference region. LIST_SUVR_REFERENCE_REGIONS is used by all command-line interfaces so you do not need to modify the pipelines' CLI to make this new region appear.

    • The path of the SUVR reference region that you will use:
    def get_suvr_mask(suvr_reference_region):
        """Get path of the SUVR mask from SUVR reference region label.
            suvr_reference_region: Label of the SUVR reference region
            Path of the SUVR mask
        import os
        suvr_reference_region_to_suvr = {
            "pons": os.path.join(
            "cerebellumPons": os.path.join(
            "pons2": os.path.join(
            "cerebellumPons2": os.path.join(
        return suvr_reference_region_to_suvr[suvr_reference_region]

    In this example, the SUVR reference region associated with the cerebellumPons label is located at <clinica>/resources/masks/region-cerebellumPons_eroded-6mm_mask.nii.gz.