Fmriprep not using fieldmap

1

Hello stars of the neurosphere,
I have a fieldmap file that fmriprep recognizes as BIDS compatible. In the “protocol_translator.json” file, I have the fieldmap correctly calling the bold files that need to be corrected, in the “intended for” field. The problem is that fmriprep isn’t using the field map. Is it a naming issue? For now I’m using the --force-syn flag, but I would like to use the field map we collected for distortion correction. Any help would be appreciated !

{
“DTI_64_DIRs_GRAPPA2”:[
“EXCLUDE_BIDS_Directory”,
“EXCLUDE_BIDS_Name”,
“UNASSIGNED”
],
“gre_field_mapping_NET”:[
“fmap”,
“acq-bold”,
[“task-rest_bold”, “task-ta2_bold”, “task-ta1_bold”]
],
“Rest_3mmiso_minTR2_2”:[
“func”,
“task-rest_bold”,
“UNASSIGNED”
],
“TA2_3mmiso_minTR2_2”:[
“func”,
“task-ta2_bold”,
“UNASSIGNED”
],
“TA_3mmiso_minTR2_2”:[
“func”,
“task-ta1_bold”,
“UNASSIGNED”
],
“MPRAGE”:[
“anat”,
“T1w”,
“UNASSIGNED”
]
}

2

Hi, Teodora. protocol_translator.json is not an BIDS concept, so fMRIPrep won’t know what to do with that.

fMRIPrep finds fieldmaps using either the IntendedFor or B0FieldIdentifier/B0FieldSource metadata. See Expressing the MR protocol intent for fieldmaps.

3

Thank you @effigies. I followed the instructions using dcm2bids.py in the bidskit. Below are the instructions. Are you suggesting I have to nix the protocol translator and create another metafile so fmriprep can recognize it?

Edit Translator Dictionary
dcm2bids.py creates a JSON series name translator in the derivatives/conversion folder. You’ll use this file to specific how you want individual series data to be renamed into the output BIDS source directory. Open the Protocol_Translator.json file in a text editor. Initially it will look something like the following, with the BIDS directory, filename suffix and IntendedFor fields set to their default values of “EXCLUDE_BIDS_Name”, “EXCLUDE_BIDS_Directory” and “UNASSIGNED” (the double quotes are a JSON requirement):

{

  • “Localizer”:[*
  •    "EXCLUDE_BIDS_Directory"*

  •    "EXCLUDE_BIDS_Name",*

  •    "UNASSSIGNED"*
  • ],*
  • “rsBOLD_MB_1”:[*
  •    "EXCLUDE_BIDS_Directory"*

  •    "EXCLUDE_BIDS_Name",*

  •    "UNASSSIGNED"*
  • ],*
  • “T1_2”:[*
  •    "EXCLUDE_BIDS_Directory"*

  •    "EXCLUDE_BIDS_Name",*

  •    "UNASSSIGNED"*
  • ],*
  • “Fieldmap_rsBOLD”:[*
  •    "EXCLUDE_BIDS_Directory"*

  •    "EXCLUDE_BIDS_Name",*

  •    "UNASSSIGNED"*
  • ],*
  • …*
    }
    The IntendedFor field is only relevant for fieldmap series and links the fieldmap to one or more EPI series for distortion correction.
4

Hi @teodorast. Sorry, I’m unfamiliar with bidskit and don’t think I can help here. I’ve added it as a tag to your post, so that it might get the attention it needs.

5

Thank you, I appreciate it!