Comments (5)
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.
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I am going to guess that it comes from the definition of mapping
(
Line 74 in cef7b1f
export_registered_b0
function (Line 25 in cef7b1f
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?
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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
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I believe this is closed by #1158, but please reopen if you see it again.
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