I wanted to know what is the best way of dealing with two anatomical scans for a single subject in a single session, for situations where the subject moved in the scanner and so a second scan was needed. How should the second scan be filed in the bids format?
Multiple runs can be indicated with the
run-XX (e.g. run-01 and run-02) label in the file name.
Hi @Miriam_Havin ,
Once you renamed your T1w scans as suggested by @Steven , you may want to write down somewhere which scan to use for your subsequent analyses (for instance use a bids-filter file as it is done for fmriprep). Tools such as fmriprep will by default merge all the input scans and this may affect your results.
There is the possibility of not including the file in the BIDS dataset at all if you are sure that neither you nor anyone else after you may want this file at all. Depending on the severity of motion, I would tend to favor this option this way you avoid a lot of downstream confusion.
If you want to still have the file in the dataset but avoid using the run entity because of possible downstream issues (like fmirprep averaging things mentioned above) you can use the
Maybe calling it
acq-motion: technically it is a bit on an “abuse” of the acquisition entity compare to its definition in the BIDS specification but it makes it more transparent from the filename what is in the file and it is definitely the kind of abuse that BIDS purist (like me) are fine with.