We are trying to process perfusion images with aslprep. The sequence is a Multi-PLD PCASL, and we have acquired the images with Siemens Magnetom Prisma. Our perfusion images are in BIDS format with 20 volumes, being 1st volume calibration image, 2nd a dummy image and then, 9 label-control pairs (aslcontext file). How could we handle this protocol? Our protocol indicate 5 PLDs (2x500, 2x1000, 2x15000, 2x2000, 2x25000). How do we have to indicate PLDs, one by one or grouped? Considering the calibration image and dummy or excluding?. You may find a screenshot of our aslcontext file.
Thank you for your assistance!
Best regards,
Lucia
Could you clarify what you mean by the “dummy” volume? Dummy volumes aren’t part of ASL-BIDS.
For the PLDs, you should have them in the PostLabelingDelay metadata field as a list of values, with one value for each volume in the ASL file. For the M0 volume, the value should be set to 0 (see here).
Thank you for your answer. We have dummy volumes in our ASL-BIDS, as you can see in the aslcontext file. We have sawn an argument (–dummy-vols) to ignore a number of initial volumes here. However, as our first image is calibration image, we don’t know how to do the dummy image, and if we have to consider PLD or not.
We managed to run one session of one participant, but we found an error while running (Node compute cbf failed to run on host neurodesktop) and when finishing it says IndexError: index 0 is out bounds for axis 0 with size 0. As a result, we did not get any cbf or perfusion data.
