✨ Use BIDS standard template identifiers for templates

[shnizzedy]

Related problem

Currently template-space files derived from C-PAC are labeled space-template which does not differentiate different-template-spaced files from one another.

Proposed feature

Use standard template identifiers like space-MNI152NLin2009

Acceptance criteria

• Each template in this repository has a defined identifier
• C-PAC uses the identifier to define the BIDS space- entity
• SpatialReference included in JSON sidecar

Alternatives

No response

Additional context

Related:

• 🚚 Merge cpac_resources.tar.gz into this repository #3
• 🚚 Give templates BIDS names #4
• 🚚 Move C-PAC templates from C-PAC into this repository #10
• 📝 Document templates included in C-PAC image fcp-indi.github.io#260
• Register MNI-space priors/ROIs to custom template C-PAC#972
• Place a check to ensure template-space tissue priors are in same space as registration templates C-PAC#1041
• 🐛 ABCD-options requires templates that aren't included in default image C-PAC#1557
• 🚚 Make correlation matrix filenames BIDSier C-PAC#1641
• 🐛 Templates don't match between monkey and nhp-macaque C-PAC#1699

[shnizzedy]

I'm backburnering in favor of FCP-INDI/TheWay#8. I case someone else picks this up before I get back to it, I started a branch (templates/MNI) that so far just adds a function (lookup_identifier) to look up the standard identifier based on a regex of the in-container filename. So far the lookup table only includes two MNI spaces.

    '''Function to return a standard template identifier for a packaged
    template, if known. Otherwise, returns the literal string
    'template'

    Parameters
    ----------
    template_path : str

    Returns
    -------
    identifier : str

    Examples
    --------
    >>> lookup_identifier('/usr/share/fsl/5.0/data/standard/'
    ...                   'MNI152_T1_1mm_brain.nii.gz')
    'MNI152NLin6ASym'
    >>> lookup_identifier('/code/CPAC/resources/templates/'
    ...                   'tpl-MNI152NLin2009cAsym_res-01_label-brain_'
    ...                   'probseg.nii.gz')
    'MNI152NLin2009cAsym'
    >>> lookup_identifier('/cpac_templates/chd8_functional_template_sk.nii')
    'template'
    '''