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AFAICT the infant_mode parameter is not being used in QSIPrepAnatomicalIngress, which is what actually collects the structural data, so even in infant mode it's looking for transforms to and from MNI152NLin2009cAsym. #123 will fix this, but I think we should push a fix ahead of time because that PR is massive.
Summary
I am trying to run qsirecon with the infant pipeline, but nipype.workflow flags the adult MNI anatomical outputs as missing.
I suspect it’s related to #44?
Additional details
What were you trying to do?
Run qsirecon with one of the built-in reconstruction workflows.
What did you expect to happen?
QSIrecon to run, since
qsirecon/qsirecon/workflows/base.py
Line 249 in 7b29424
suggests that there is a switch built in for —infant with the MNI Infant template.
What actually happened?
Reproducing the bug
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