Hi all,
I am hoping to use ASLPrep to process an ASL data set that I have, but I am encountering an issue with getting our ASL sequence into BIDS format. The data was collected on a 3T Siemens Prisma scanner, and the output file is structured as an M0 volume, a dummy volume, and then 9 label-control pairs, but the current BIDS specification for the aslcontext.tsv file does not seem to have any option for indicating a dummy volume, just label/control/m0.
I tried to resolve this issue by using fslroi to extract the M0 into a separate m0scan.nii.gz file and remove the M0 and dummy from asl.nii.gz, and duplicating the json file (adding the BIDS-required fields for each image after duplication); however, this results in the BIDS validator flagging an error that “The number of volumes in the ‘_aslcontext.tsv’ for this file does not match the number of values in the NIfTI header.” Running fslinfo gives the correct number of volumes for the m0 (1) and asl (18).
Does anyone know how to either encode dummy volumes in aslcontext.tsv in a way that is BIDS compliant and would work with ASLPrep (preferred solution), or modify the nifti headers somehow to make it reflect the new file structure?
Thanks!