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I am working on a graduate research project using the ABIDE I and II autism datasets.

MRIQC has been run on these data - and I now must remove participants marked as outliers on 3 specific quality metrics. However, I have run into an issue - there appear to be multiple "runs" per participant.

If, on one run, the participant fails QC stipulations, but not on another run, does this mean that the participant should be excluded from analyses? Or is the purpose of having multiple "runs" in structural MRI in order to have sufficient data that, if one run is "bad", another run can be used?

I have tried reading the MRIQC documentation; Googling; downloading and reading textbooks - for some reason, I find numerous resources on fMRI, but nothing for structural.

I would really appreciate any help anyone can offer - I am a bit desperate at this stage as my supervisors are on holiday.

Thank you for reading.

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It is common to remove especially motion-corrupted MRI runs without excluding the subject.

Without more knowledge about the project it's hard to know why exactly they have multiple runs present and whether there are differences between runs or just repeated scans. It may be that the operators made sure to collect more data when they suspected subjects had too much motion during the scan, they may have done so randomly or by convenience (such as according to patient comfort), or they may have had other reasons.

I would consult other papers published using the same data set (even the functional ones) for their inclusion criteria.

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