Defining standard and nonstandard spaces where data will be resampled

The command line interface of PETPrep allows resampling the preprocessed data onto other output spaces. That is achieved using the --output-spaces argument, where standard and nonstandard spaces can be inserted.

Important

PETPrep writes derivatives only for the output spaces listed in --output-spaces. Some options may add internal spaces required by the workflow, but those spaces are not written as derivatives unless they are also requested explicitly.

TemplateFlow

TemplateFlow is a software library and a repository of neuroimaging templates that allows end-user applications such as PETPrep to flexibly query and pull template and atlas information. In other words, TemplateFlow enables PETPrep to access a wide range of templates (and also custom templates, see below). Therefore, TemplateFlow is central to define PETPrep’s interface regarding template and atlas prior-knowledge. For more general information about TemplateFlow, visit TemplateFlow.org.

Standard spaces

When using PETPrep in a workflow that will investigate effects that span across analytical groupings, neuroimagers typically resample their data onto a standard, stereotactic coordinate system. The most widely used standard space for PET analyses is generally referred to as MNI. For instance, to instruct PETPrep to use the MNI template brain distributed with FSL as coordinate reference the option will read as follows: --output-spaces MNI152NLin6Asym. By default, PETPrep writes derivatives in MNI152NLin2009cAsym at native PET resolution and in the individual anatomical reference (T1w). Valid template identifiers (MNI152NLin6Asym, MNI152NLin2009cAsym, etc.) come from the TemplateFlow repository.

For each requested standard output space, PETPrep will resample the preprocessed PET data into that space, labeling the corresponding outputs with the space-<template-identifier> BIDS entity. By default, the resampled outputs keep the original resolution of the PET data to produce smaller files, more consistent with the original data gridding. However, many users will be interested in utilizing a coarse gridding (typically 2mm isotropic) of the target template. Such a behavior can be achieved applying modifiers to the template identifier, separated by a : character. For instance, --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym will generate preprocessed PET 4D files on two standard spaces (MNI152NLin6Asym, and MNI152NLin2009cAsym) with the template’s 2mm isotropic resolution for the data on MNI152NLin6Asym space and the original PET resolution (say, e.g., 2x2x2.5 [mm]) for the case of MNI152NLin2009cAsym. This is equivalent to saying --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-native.

Danger

Please remember that the resolution entity of TemplateFlow is an index, and therefore, res-2 does not necessarily mean 2mm isotropic - although, it coincidentally does in the example above. However, it may not be the case. For instance, MNI152NLin6Asym:res-3 contains a template with 0.5mm isotropic voxels.

Other possible modifiers are, for instance, the cohort selector. For instance, --output-spaces MNIPediatricAsym:res-1:cohort-2 selects the resolution 1 of cohort-2 which, for the MNIPediatricAsym template, corresponds to the prepuberty phase (4.5–8.5 years old).

Space modifiers such as res are combinatorial: --output-spaces MNIPediatricAsym:cohort-1:cohort-2:res-native:res-1 will generate conversions for the following combinations:

  • cohort 1 and “native” resolution (meaning, the original PET resolution),

  • cohort 1 and resolution 1 of the template,

  • cohort 2 and “native” resolution (meaning, the original PET resolution), and

  • cohort 2 and resolution 1 of the template.

Please mind that the selected resolutions specified must exist within TemplateFlow.

When specifying surface spaces (e.g., fsaverage), the legacy identifiers from FreeSurfer will be supported (e.g., fsaverage5) although the use of the density modifier would be preferred (i.e., fsaverage:den-10k for fsaverage5).

Custom standard spaces

To make your custom templates visible by PETPrep, and usable via the --output-spaces argument, please store your template under TemplateFlow’s home directory. The default TemplateFlow’s home directory is $HOME/.cache/templateflow and that path can be changed by setting the $TEMPLATEFLOW_HOME environment variable. A minimal example of the necessary files for a template called MyCustom (and therefore callable via, e.g., --output-spaces MyCustom) follows:

$TEMPLATEFLOW_HOME/
    tpl-MyCustom/
        template_description.json
        tpl-MyCustom_res-1_T1w.nii.gz
        tpl-MyCustom_res-1_desc-brain_mask.nii.gz
        tpl-MyCustom_res-2_T1w.nii.gz
        tpl-MyCustom_res-2_desc-brain_mask.nii.gz

For further information about how custom templates must be organized and corresponding naming, please check the TemplateFlow tutorials.

Nonstandard spaces

Additionally, --output-spaces accepts identifiers of spatial references that do not generate standardized coordinate spaces:

  • T1w or anat: data are resampled into the individual’s anatomical reference generated with the T1w and T2w images available within the BIDS structure.

  • fsnative: similarly to the anat space for volumetric references, including the fsnative space will instruct PETPrep to sample the original PET data onto FreeSurfer’s reconstructed surfaces for this individual.

  • petref requests PET data in the PET reference grid. For multi-frame PET series, the preprocessed PET output is resampled into this grid with head-motion correction applied.

Modifiers are not allowed when providing nonstandard spaces.

Preprocessing blocks depending on standard templates

Some modules of the pipeline operate in specific template spaces even when those spaces are not requested as derivatives. PETPrep always adds MNI152NLin2009cAsym to the internal list of spaces because several workflows require that anatomical normalization. If CIFTI outputs are requested with --cifti-output, PETPrep also adds MNI152NLin6Asym internally at the resolution required by the selected grayordinates density.

Atlas-based segmentation options selected with --seg may also add the corresponding atlas template to the list of spaces so that the atlas and its labels can be warped into anatomical space.

Spaces added only to satisfy these workflow requirements are used internally. They are not written as PET derivatives unless the space was also explicitly requested with --output-spaces.