Issues with setting max_bval about pyafq HOT 5 CLOSED

My guess, based on this error, is that we have a bug that has to do with the b-value threshold being applied in some places, but not in others, so you get this kind of mismatch here. Unfortunately, I am not going to have time to look into this more closely before Friday at the very earliest.

from pyafq.

I am going to guess that it comes from the definition of mapping (

def mapping(base_fname, dwi_data_file, reg_subject, data_imap,
            mapping_definition=None):
    """
    mapping from subject to template space.

    Parameters
    ----------
    mapping_definition : instance of `AFQ.definitions.mapping`, optional
        This defines how to either create a mapping from
        each subject space to template space or load a mapping from
        another software. If creating a map, will register reg_subject and
        reg_template.
        If None, use SynMap()
        Default: None
    """
    reg_template = data_imap["reg_template"]
    if mapping_definition is None:
        mapping_definition = SynMap()
    if not isinstance(mapping_definition, Definition):
        raise TypeError(
            "mapping must be a mapping defined"
            + " in `AFQ.definitions.mapping`")
    return mapping_definition.get_for_subses(
        base_fname, data_imap["dwi"], dwi_data_file,
        reg_subject, reg_template)

Perhaps the DWI from data_imap["dwi"] becomes mismatched with dwi_data_file when the b_val thresholding is applied?

from pyafq.

Yes, this is correct, in fact, dwi_data_file probably should not be used anywhere in the pimms system outside of its initial use where are the bval selections happen and the orientation happens. Afterwards it should just be dwi. I am going to review and change uses of them, then open a PR, and we'll see if that fixes it

from pyafq.

I was able to reproduce and fix the bug. Its not in the mapping code as it just uses that file path as a reference for BIDS to find other files. But it was a similar idea in the calculation of the b0. Here is the PR, if it passes all tests we can merge it: #1158

from pyafq.

I believe this is closed by #1158, but please reopen if you see it again.

from pyafq.