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pet-volume – Volume-based processing of PET images

This pipeline performs several processing steps on PET data in voxel space, which include:

  • intra-subject registration of the PET image into the space of the subject’s T1-weighted MR image using SPM;
  • (optional) partial volume correction (PVC) using the PETPVC toolbox [Thomas et al., 2016];
  • inter-subject spatial normalization of the PET image into MNI space based on the DARTEL deformation model of SPM [Ashburner, 2007];
  • intensity normalization using the average PET uptake in reference regions resulting in a standardized uptake value ratio (SUVR) map;
  • parcellation into anatomical regions based on an atlas and computation of average values within each region. The list of available atlases can be found here.

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.


You need to have performed the t1-volume pipeline on your T1-weighted MR images.


  • If you only installed the core of Clinica, this pipeline needs the installation of SPM12. You can find how to install this software package on the third-party page.

  • If you want to apply partial volume correction (PVC) on your PET data, you will need to install PETPVC 1.2.4, which depends on ITK 4. More information on the third-party page.

Running the pipeline

The pipeline can be run with the following command line:



  • BIDS_DIRECTORY is the input folder containing the dataset in a BIDS hierarchy.
  • CAPS_DIRECTORY acts both as an input folder (where the results of the t1-volume-* pipeline are stored) and as the output folder containing the results in a CAPS hierarchy.
  • GROUP_LABEL is the label of the group that is associated to the DARTEL template that you had created when running the t1-volume pipeline.
  • ACQ_LABEL is the label given to the PET acquisition, specifying the tracer used (trc-<acq_label>).
  • The reference region is used to perform intensity normalization (i.e. dividing each voxel of the image by the average uptake in this region) resulting in a standardized uptake value ratio (SUVR) map. It can be cerebellumPons or cerebellumPons2 (used for amyloid tracers) or pons or pons2 (used for FDG).

Pipeline options:

  • --pvc_psf_tsv: TSV file containing the psf_x, psf_y and psf_z of the PSF for each PET image. More explanation is given in PET Introduction page.
  • --smooth: a list of integers specifying the different isotropic full width at half maximum (FWHM) in millimeters to smooth the image. Default value is: 0, 8 (both without smoothing and with an isotropic smoothing of 8 mm)


Since the release of Clinica v0.3.8, the handling of PSF information in the TSV file has changed: fwhm_x, fwhm_y, fwhm_z columns have been replaced by psf_x, psf_y, psf_z and the acq_label column has been added. Additionally, the SUVR reference region is now a compulsory argument: it will be easier for you to modify Clinica if you want to add a custom reference region (PET Introduction page). Choose cerebellumPons for amyloid tracers or pons for FDG to have the previous behavior.


The arguments common to all Clinica pipelines are described in Interacting with clinica.


Do not hesitate to type clinica run pet-volume --help to see the full list of parameters.


Results are stored in the following folder of the CAPS hierarchy: subjects/<participant_id>/<session_id>/pet/preprocessing.

The main output files are:

  • <source_file>_space-T1w[_pvc-rbv]_pet.nii.gz: PET image registered into the T1-weighted MRI native space.

  • <source_file>_space-Ixi549Space[_pvc-rbv]_suvr-<label>_mask-brain[_fwhm-<X>mm]_pet.nii.gz: standard uptake value ratio (SUVR) PET image in MNI space, masked to keep only the brain, and optionally smoothed.

  • atlas_statistics/<source_file>_space-<space>[_pvc-rbv]_suvr-<label>_statistics.tsv: TSV files summarizing the regional statistics on the labelled atlas <space>.


The [_pvc-rbv] label indicates whether the PET image has undergone partial value correction (region-based voxel-wise method) or not.

The full list of output files from the pet-volume pipeline can be found in the The ClinicA Processed Structure (CAPS) specifications.

Going further

Describing this pipeline in your paper

Example of paragraph:

Theses results have been obtained using the pet-volume pipeline of Clinica [Routier et al., 2021; Samper et al., 2018]. This pipeline first performs intra-subject registration of the PET image into the space of the subject’s T1-weighted MR image using SPM. [The PET image is corrected for partial volume effects using the PETPVC toolbox [Thomas et al., 2016].] The PET image is then spatially normalized into MNI space using the DARTEL deformation model of SPM, and intensity normalized using the average PET uptake in a reference region ([pons | pons + cerebellum]). Finally, the average PET uptake is computed for a set of regions obtained from different atlases in MNI space [Tzourio-Mazoyer et al., 2002, 2015; Joliot et al., 2015; Hammers et al., 2003; Gousias et al., 2008; Shattuck et al., 2008; CAT12].


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