Location of output images when session is present & ignored about fitlins HOT 11 CLOSED

Okay. The main reason I suggest it is that the output directories have the potential to get very full, and separating run-level from higher-level results might help significantly declutter. But we can always circle back to it later if that does turn out to be an issue.

from fitlins.

As an example, here is a filename ses-movie_task-movie_run-1_bold_contrast-framewiseDisplacement_stat.nii.gz

From this, I gather session is higher in the hierarchy than task and that's why it gets its own folder?

from fitlins.

Yeah, I think that's true. Are there any cases where we would want to preserve session outside the subject?

from fitlins.

One way to address this might be to dump a small JSON file in each output directory (if we're not already doing this) that contains metadata that makes it clear what the folder represents. E.g., "Level": "dataset".

from fitlins.

I think the meta-data file helps.
I'm not so concerned about preserving session, as much as I think the dataset level stuff should be in the same place regardless. And actually, I think since dataset level supersedes session, it should probably not be preserved. If you wanted to do a session level analysis, that would be a contrast at the dataset level, correct?

from fitlins.

That's a little difficult because sometimes you have multiple levels in the same directory, as there's no provision in BIDS for new subdirectories. Would it make sense to have level-X as a key/value pair in the filename? That might help with things like:

sub-01_task-nback_run-1_contrast-maineffect_zscore.nii.gz
sub-01_task-nback_run-2_contrast-maineffect_zscore.nii.gz
sub-01_task-nback_contrast-maineffect_zscore.nii.gz

It could be:

sub-01_task-nback_run-1_level-run_contrast-maineffect_zscore.nii.gz
sub-01_task-nback_run-2_level-run_contrast-maineffect_zscore.nii.gz
sub-01_task-nback_level-subject_contrast-maineffect_zscore.nii.gz

from fitlins.

That's pretty ugly, but has the benefit of being unambiguous, so I guess I'd go with it. Alternatively, we could drop that info in the sidecars (but I guess those won't contain anything else otherwise, so probably no reason to create them just for that).

from fitlins.

Sidecars will still want SourceFile at minimum.

But the only place where we really run into this right now is the run level, because all other levels have corresponding directories. What if we add a level-run subdirectory that can sit inside the subject or session subdirectory?

sub-01/
    [ses-01]/
        level-run/
            sub-01_[ses-01_]task-nback_run-1_contrast-maineffect_zscore.nii.gz
        [sub-01_ses-01_task-nback_contrast-maineffect_zscore.nii.gz]
    sub-01_task-nback_contrast-maineffect_zscore.nii.gz
sub-02/
    ...
task-nback_contrast-maineffect_zscore.nii.gz

It's not spec compliant, but neither are our suffixes.

from fitlins.

If we have sidecars anyway, then I'd vote to put Level in there, and probably to make it mandatory for all images (whether or not the context is sufficient to determine level). That way we can be fully compliant and still eliminate any ambiguity. I'm not crazy about a level-run subfolder because I think it will throw some users for a loop the first time they see it.

from fitlins.

from fitlins.

Maybe we should call it BIDSStatsModelLevel or at least AnalysisLevel for clarity.

from fitlins.