None of the available B0 fieldmaps

[Jon_Brooks]

Hi All ( @Steven )

I’m still trying to get to grips with formatting my .json file for dcm2bids to make sense of some DICOM data. In particular, I’m struggling with applying fieldmaps to the relevant scans…

When I’m running fmriprep I’m getting the following warning:

None of the available B0 fieldmaps are associated to </gpfs/data/uwwbic/gnx20mmu/dcm2bids-proj/MEMAG/sub-MRC204/func/sub-MRC204_task-recall_bold.nii.gz>
240304-18:45:03,500 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.931s.
240304-18:45:03,647 nipype.workflow INFO:
	 No single-band-reference found for sub-MRC204_task-rest_bold.nii.gz.
240304-18:45:03,647 nipype.workflow CRITICAL:
	 None of the available B0 fieldmaps are associated to </gpfs/data/uwwbic/gnx20mmu/dcm2bids-proj/MEMAG/sub-MRC204/func/sub-MRC204_task-rest_bold.nii.gz>

I’ve followed guidance from the dcm2bids config page, and it’s not immediately obvious what I’m doing wrong…?

Here’s the offending .json file used for conversion:

{
  "descriptions": [
	{
      "datatype": "anat",
      "suffix": "T1w",
      "criteria": {
        "SeriesDescription": "MPRAGE GRAPPA2"
      }
    },
	{
      "datatype": "anat",
      "suffix": "T2w",
      "custom_entities": "acq-TE1",
      "criteria": {
        "SeriesDescription": "TSE_3TE_Cor_Hippo",
        "EchoTime": 0.0095
      }
    },
	{
      "datatype": "anat",
      "suffix": "T2w",
      "custom_entities": "acq-TE2",
      "criteria": {
        "SeriesDescription": "TSE_3TE_Cor_Hippo",
        "EchoTime": 0.076
      }
    },
	{
      "datatype": "anat",
      "suffix": "T2w",
      "custom_entities": "acq-TE3",
      "criteria": {
        "SeriesDescription": "TSE_3TE_Cor_Hippo",
        "EchoTime": 0.143
      }
    },
	{
      "id": "task-rest",
      "datatype": "func",
      "suffix": "bold",
      "custom_entities": "task-rest",
      "criteria": {
        "SeriesDescription": "rest_cmrr_mbep2d"
	  },
      "sidecar_changes": {
        "TaskName": "rest"
      }
    },
	{
      "id": "task-recall",
      "datatype": "func",
      "suffix": "bold",
      "custom_entities": "task-recall",
      "criteria": {
        "SeriesDescription": "task_cmrr_mbep2d"
	  },
      "sidecar_changes": {
        "TaskName": "recall"
      }
    },
	{
      "datatype": "fmap",
	  "suffix": "magnitude1",
	  "IntendedFor": [
		4,
		5
	  ],
      "criteria": {
        "EchoNumber": "1",
		"EchoTime": 0.00492
      }
    },
	{
      "datatype": "fmap",
	  "suffix": "magnitude2",
	  "IntendedFor": [
		4,
		5
	  ],
      "criteria": {
        "EchoNumber": "2",
		"EchoTime": 0.00738,
		"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"]
      }
    },
	{
      "datatype": "fmap",
	  "suffix": "phasediff",
	  "IntendedFor": [
		4,
		5
	  ],
      "criteria": {
        "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"]
      },
	  "sidecar_changes": {
		"EchoTime1": 0.00492,
        "EchoTime2": 0.00738,
		"B0FieldIdentifier": "phasediff_fmap0"
      }
    },
	{
      "datatype": "dwi",
      "suffix": "dwi",
      "custom_entities": "dir-AP",
      "criteria": {
        "SeriesDescription": "cmrr_mbep2d_diff_60B07_AP"
      }
    },
	{
      "datatype": "dwi",
      "suffix": "dwi",
      "custom_entities": "dir-PA",
      "criteria": {
        "SeriesDescription": "cmrr_mbep2d_diff_60B07_PA"
      }
    }
]
}

Any help would be much appreciated.

Cheers, Jon