Hi all,
I have been reading multiple threads on similar issue but none of the previous solutions worked.
I have inherited a children task fMRI dataset. The results on SPM were subpar due to high signal noise and I was curious if I could do better using fmriprep. I would like to run ICA-AROMA on the dataset, so my working fmriprep version is 23.0.1. I am kind of lost because I have used this fmriprep version before on other datasets (rest data) and the correction was always applied. There, IntendedFor value was set to
{
"IntendedFor": "bids::sub-01/ses-Scan2postECT/func/sub-01_ses-Scan2postECT_task-rest_run-1_part-mag_bold.nii.gz"
}
with direct fieldmapping.
Now I have a single pepolar image but no matter the IntendedFor definition, fmap is never located and fmriprep finishes without it. BIDS validation only passed a single IntendedFor value:
{"IntendedFor": "ses-1/func/sub-1005_ses-1_task-sst_part-mag_bold.nii.gz"}
Here is the subject tree I am testing on:
sub-1005
└── ses-1
├── anat
│ ├── sub-1005_ses-1_T1w.json
│ └── sub-1005_ses-1_T1w.nii.gz
├── beh
│ ├── sub-1005_ses-1_task-sst_beh.tsv
│ └── sub-1005_ses-1_task-ts_beh.tsv
├── fmap
│ ├── sub-1005_ses-1_acq-sst_dir-pa_epi.json
│ └── sub-1005_ses-1_acq-sst_dir-pa_epi.nii.gz
└── func
├── sub-1005_ses-1_task-sst_events.tsv
├── sub-1005_ses-1_task-sst_part-mag_bold.json
└── sub-1005_ses-1_task-sst_part-mag_bold.nii.gz
fmap json should hold all information:
{
"Manufacturer": "Philips",
"PatientPosition": "HFS",
"SeriesDescription": "ImageMRSERIES",
"ProtocolName": "WIPSST_PA_s1SENSE",
"SeriesNumber": 8,
"AcquisitionNumber": 8,
"ImageComments": "TECTO",
"PhilipsRescaleSlope": 0.75018,
"PhilipsRescaleIntercept": 0,
"PhilipsScaleSlope": 0.00316373,
"UsePhilipsFloatNotDisplayScaling": 1,
"EchoTime": 0.03,
"RepetitionTime": 1.7,
"ImageOrientationPatientDICOM": [
0.999517,
0.00774078,
-0.0300964,
-0.0116886,
0.991007,
-0.133297
],
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220720",
"PhaseEncodingDirection": "j-",
"SliceThickness": 2.5,
"EffectiveEchoSpacing": 0.0005842639489512227,
"TotalReadoutTime": 0.0461568519671466,
"IntendedFor": "ses-1/func/sub-1005_ses-1_task-sst_part-mag_bold.nii.gz",
"TaskName": "sst"
}
Does anyone have any solutions? Thank you