Hello,
I am running into an error with the intendedfor field in the fieldmap.json files. Fmriprep runs fine when I have one functional file in the intendedfor field as follows:
"IntendedFor": "ses-00/func/sub-01_ses-00_task-unfunc_run-03_bold.nii.gz",
However as soon as I try to use it on more than one functional file like this:
"IntendedFor": ["ses-00/func/sub-01_ses-00_task-unfunc_run-03_bold.nii.gz",
"ses-00/func/sub-01_ses-00_task_unfunc_run-04_bold.nii.gz"],
I get this error that says that
1: [ERR] ‘IntendedFor’ field needs to point to an existing file. (code: 37 - INTENDED_FOR)
./sub-01/fmap/sub-01_acq-topup_dir-AP_epi.nii.gz
Evidence: ses-00/func/sub-01_ses-00_task_unfunc_run-04_bold.nii.gz
All the files exist and the error only occurs for the second specified functional run (i.e. run04), not the one on the first line (i.e. run03). If I switch which run is specified on which line then the error pops up or run03 so this has to do with how fMRIprep is reading the json file not with the actual file locations.
Any suggestions?