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nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
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Apply MRIQC on previously skull-stripped 3D-T1w #909

Closed RocaVincent closed 3 years ago

RocaVincent commented 3 years ago

Hello

Is it a problem to use MRIQC with previously skull stripped 3D-T1 (volBrain) ? And if it is, what can I do to avoid having biased results ?

oesteban commented 3 years ago

Is it a problem to use MRIQC with previously skull stripped 3D-T1 (volBrain) ?

Yes, MRIQC doesn't work on skull stripped images. Many of the quality metrics will look at portions of the background, which in this case will be all-zeros.

And if it is, what can I do to avoid having biased results ?

The only thing you could do is redefine "results", and don't use MRIQC in this case.

MRIQC is for raw images (although defaced images are supported for obvious reasons). If the quality assessment you intend to do is on preprocessed data, then you should use some other tool. There are many out there (e.g., https://incf.github.io/niQC/tools).