T2starmaps with splendid multiband boundaries

[jaetzel]

Good catch! Those are indeed noise volumes: “EPI noise scans” is 3. We also have separate phase “runs” (I’m not sure what exactly to call them; a full set of “Pha” dicoms are written for each functional run), which look quite different and I haven’t been using them in preprocessing (yet). I have been including the pair of spin-echo fieldmaps (with B0FieldIdentifier & B0FieldSource in the jsons).

Something Wrong With Functional Files after fMRIPrep (As Shown in fMRIPrep .html Outputs)

The easiest way to check would be to look at your protocol PDF (assuming your data come from a Siemens scanner). With the CMRR MB-EPI sequence, you can find the value of the “EPI noise scans” field under the “Sequence - Special” card. If it’s > 0, then you have noise scans at the end of the scan. Otherwise, you can look at the files with an image viewer (e.g., fsleyes). If you go to the last volume in the series, it should look basically like white noise instead of a brain if it’s a noise scan.…

I was thinking I could do a quick test by deleting the last dozen dicoms (this run has three echoes) before running dcm2niix … but that’s not getting rid of them all, so I’ll dig into the documentation after lunch and see if I can figure out how to properly handle these.

Thanks!