✨ Freesurfer-Ingress without data config

[nx10]

Related problem

I am running a large batch of different pipeline configs, some of which will be re-using freesurfer ingress-ed data between them.

Right now freesurfer ingress can only be used when also using a data config file (docs) and modifying both of them which over-complicates this process a little.

Building scripts for each subject-session combination in a large dataset requires to copy around the following paths:

graph TD
    a[BIDS subject-session]
    t[T1w]
    b[BOLD]
    f[Freesurfer CLI]
    d[C-PAC data config]
    p[C-PAC pipeline config]
    c[C-PAC CLI]

    a --> t
    a --> b
    t --> f
    t --> d
    f --> d
    b --> d
    d --> c
    p --> c
    a -.->|Unused but need to\n specify because of BIDS App| c

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Proposed feature

It would be nice if C-PAC would accept a command line flag (e.g. --ingress-freesurfer [PATH]) and would find the rest of the data in the BIDS input dir as usual instead of having to supply an extra data config.

This would simplify the graph to this:

graph TD
    a[BIDS subject-session]
    t[T1w]
    f[Freesurfer CLI]
    p[C-PAC pipeline config]
    c[C-PAC CLI]

    a --> t
    t --> f
    f --> c
    p --> c
    a --> c

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Acceptance criteria

• Data configs does not need to be created to use freesurfer ingress

Alternatives

No response

Additional context

No response