T1w-dwiref co-registration refinement with brain masks #979
Description
Summary
The co-registration of ACPC space preprocessed T1w and dwiref images from QSIPrep (v1.0.1) appears to be significantly shifted along the inferior-superior axis for some of the 7 Tesla data collected at our site (see below)
To address this offset, the brain masks for each respective image can be supplied to antsRegistration to prevent unwanted alignment of CSF/dura from the b0 image to skull in the T1w image. The images below are from the same dataset, after antsRegistration using the options specified in QSIPrep and the additional -x / --masks command-line argument.
coreg_masked.webm
Additional details
This additional masked registration was performed with existing outputs from QSIPrep.
Next steps
There are two options that could accomplish this end:
- Supply brain masks as an option in the co-registration step.
- Use a skull-stripped brain for the dwiref image to match the node input name
ref_b0_brain.