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nipreps / dmriprep

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://www.nipreps.org/dmriprep
Apache License 2.0
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SDC - Horrible co-registration of *b=0* reference and EPI reference #168

Open oesteban opened 3 years ago

oesteban commented 3 years ago

The inputs to antsRegistration when finding the misalignment between the fieldmap reference and the target DWI (via its b=0 reference) is currently unacceptable for our dataset ds001771.

This problem is very likely to be present in any dataset, as the b=0 reference we are using right now (work/dmriprep_wf/single_subject_36_wf/dwi_preproc_acq_AP_wf/dwi_reference_wf/enhance_and_skullstrip_dwi_wf/normalize/normalized.nii.gz) is definitely suboptimal.

Perhaps, we should move towards the new reference workflow in niworkflows, if we haven't done so yet.

oesteban commented 3 years ago

Seems to be fixed in #169 with production settings, but still problematic for ds001771 in debug settings.