Naming unfinished and restarted MRI runs of a task in BIDS


I am very new to fmriprep and have a question regarding the appropriate labeling of task runs that were unfinished and then restarted.

In my experiment I have six identical blocks, each containing one four different tasks / miniblocks.
In two of my subjects the scanner stopped working in the middle of the third miniblock of run 5. Luckily, my script waits for scanner pulses at the start of a new miniblock. So I waited for the miniblock to end and then restarted the scanner and continued with the final miniblock.
That means I now have two files for run 5, one containing the beginning, the other the last task.

Now this seems to have made it a bit tricky to name the nifti files.
I found a way to get it to run but only by naming them a bit awkwardly.


Ideally, I would love to add something after run-05 like run-05-EncodingOddEven.
But then computer says no.

Also since there is theoretically only one maintaskEncodingOddEven, from a logical perspective this would suggest, that run-05 is incorrect and should be run-01 instead. But I hope people will understand. Or will I run into issues later?

Hi @Frederik_Bergmann and welcome to Neurostars!

I would save these this split as run-5 and run-6, and then have a note in the BIDS README file describing this situation so you and others are aware. You can also add an acq-<> label, such as acq-part1 or whatever would make sense to you, to indicate in the filename that this is before/after a scanner break.


1 Like