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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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questions about MRIQC (use output of other pipeline; reports for other MRI image; test example) #791

Closed s165838 closed 5 years ago

s165838 commented 5 years ago

Hi all,

I am a beginner and have several questions about MRIQC. 1) How to run MRIQC using the outputs from another pipeline that didn’t use the MRIQC workflow? 2) Can MRIQC generate qualitative reports for other MRI contrasts (besides anatomical and functional), such as diffusion MRI, QSM MRI? 3) Where can I get an test example of MRIQC. I appreciate very much for your time.

Best,

Zhiguo

oesteban commented 5 years ago

1) How to run MRIQC using the outputs from another pipeline that didn’t use the MRIQC workflow?

That is not possible by design. MRIQC only works on original data. The only acceptable preprocessing step is defacing (i.e. removing facial features from anatomical scans) for HIPAA/GDPR requirements.

2) Can MRIQC generate qualitative reports for other MRI contrasts (besides anatomical and functional), such as diffusion MRI, QSM MRI?

It can't. We would be very happy to incorporate such extensions, should someone contribute them.

3) Where can I get an test example of MRIQC

If you want data to run MRIQC on your own, https://openneuro.org has lots of datasets in the right BIDS format. If you want to see examples of reports generated by MRIQC -> https://mriqc.s3.amazonaws.com/index.html#openfmri/