SR reports generation without brain masks

Medical-Image-Analysis-Laboratory / fetmrqc

FetMRQC is a tool for quality assessment (QA) and quality control (QC) of T2-weighted (T2w) fetal brain MR images.

Apache License 2.0

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Open t-sanchez opened 4 months ago

t-sanchez commented 4 months ago

Not all SR reconstruction models are able to give a brain mask. This means that:

list_bids and report generation should be able to work without masks.
this could be more problematic for the IQMs extraction. An option could be to rely on tools like SynthStrip to skull-strip the SRR. This should be integrated automatically somewhere in the pipeline when no masks are given.

t-sanchez commented 4 months ago

Done with list_bids in #30