Support session-wise post-processing

[tsalo]

Summary

Anatomical processing is done across sessions. Power users work around this by using the --bids-filter-file to run each session separately, but we should natively support session-wise processing.

[cindyhfls]

The link to the example JSON file for this flag is broken. Can you fix that? https://xcp-d.readthedocs.io/en/latest/usage.html. What should be the argument used to run each session separately

[tsalo]

I've opened #1323 to fix the link.

I don't think we'll have an argument on XCP-D's end to enably session-wise processing. It should depend on the organization of the input data.

[cindyhfls]

Thanks.

So if I do:

{
   "bold": {
      "session": ["01","02"],
      "task": ["rest"]
   }
}

It would try to use the same anatomical file, but if I do:

{
   "bold": {
      "session": ["01"],
      "task": ["rest"]
   }
}

and run the pipeline again on

{
   "bold": {
      "session": ["02"],
      "task": ["rest"]
   }
}

Then it's okay?

[tsalo]

You should probably include "session": ["01"] for all of the entries in https://github.com/PennLINC/xcp_d/blob/7694faa6fcbe0f5ed3d9ab0bf272f7ecedaf5a0d/xcp_d/data/io_spec.yaml.

[cindyhfls]

I don't quite follow that, can you provide a toy example of how this --bids-filter-file is used?

[tsalo]

Something like this

{
    "anat_brainmask": {
        "session": "01"
    },
    "anat_to_template_xfm": {
        "session": "01"
    },
    "bold": {
        "session": "01"
    },
    "cortical_thickness": {
        "session": "01"
    },
    "cortical_thickness_corr": {
        "session": "01"
    },
    "lh_pial_surf": {
        "session": "01"
    },
    "lh_subject_sphere": {
        "session": "01"
    },
    "lh_wm_surf": {
        "session": "01"
    },
    "myelin": {
        "session": "01"
    },
    "myelin_smoothed": {
        "session": "01"
    },
    "rh_pial_surf": {
        "session": "01"
    },
    "rh_subject_sphere": {
        "session": "01"
    },
    "rh_wm_surf": {
        "session": "01"
    },
    "sulcal_curv": {
        "session": "01"
    },
    "sulcal_depth": {
        "session": "01"
    },
    "t1w": {
        "session": "01"
    },
    "t2w": {
        "session": "01"
    },
    "template_to_anat_xfm": {
        "session": "01"
    }
}

[mattcieslak]

@tsalo wdyt about adding --session-id for session filtering?

[tsalo]

That should definitely be part of this.