Question about heudiconv


I’m collecting fMRI data for my experiments.Typically, the collected data is an integer multiple of TR(e.g. 600s for TR=2000ms, so there are 300 TRs or volumes). Due to the peculiarities of the experiment, I set a scan time long enough and then manually stopped the scanner when the participant had completed the task. This results in the acquired data stopping at a slice within a TR or volume. In other words, the last TR or volume may be incomplete.

Can heudiconv directly handle the data in this case?Or do I need to do something manually before?


it will likely be dcm2niix which would be unhappy some times but not always. See dcm2niix node does not error out whenever dcm2niix exits with 1 · Issue #3592 · nipy/nipype · GitHub . So overall

  • I would have advised to avoid doing so
  • depending on your scanner, if dcm2niix can convert incomplete sequences where it is just not all dynamics, I would advise to write a little script to first cleanup your dicom folders and remove/move those incomplete volumes away so dcm2niix could convert without failing