I have a general question. So when you do dcm2niix bids conversion before running participants through MRIQC, how do other people go about flagging subjects to double check?
Do you guys flag subjects that don’t meet the number of runs? (i.e., if you are expecting 2 runs of each bold task and a subject had 3 runs because the first one failed, or flagging because of volume in nifti files).
I just would like some advice on how to best go about looking for which subjects to manually look over/check before I run everyone through MRIQC.
Also if anyone has any advice on how they went about writing code for which subjects to flag that would be great (I mainly use Python).
Thanks. I’ll look into that, but with regards to analysis, we are running MRIQC and then fmriprep analysis. So just before running MRIQC what checks do people run on BIDS dataset apart from the validator? My files are all bids valid.
The BIDS validator should catch a lot of errors. I guess you could also make sure each subject has at least the required files (T1w and BOLD, fmaps with IntendedFor/B0FieldIdentifer if collected). ChatGPT should do a good job of making a script for you.
Do you guys flag subjects that don’t meet the number of runs? (i.e., if you are expecting 2 runs of each bold task and a subject had 3 runs because the first one failed, or flagging because of volume in nifti files).
The BIDS validator used to give a warning if subjects had differing numbers of runs for different tasks. I haven’t used the validator in a bit, but that might save you some coding if that’s still a function.
