Qsiprep disregards fieldmaps

Summary of what happened:

My data was in BIDS format. In addition to the DWI data, I acquired a field map, which was a b0 image with the inverse phase-encoding direction. However, in the final HTML report, I noticed that the susceptibility distortion correction was not applied.

Command used (and if a helper script was used, a link to the helper script or the command generated):

singularity run  /xxx/qsiprep-1.0.0.sif    /xxx/bids   /output  participant --participant-label sub-LM001  --fs-license-file /xxx/license.txt --output-resolution 1.8

Version:

QSIPrep 1.0.0

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

├── anat
│ ├── sub-LM001_ses-T1_T1w.json
│ └── sub-LM001_ses-T1_T1w.nii.gz
├── dwi
│ ├── sub-LM001_ses-T1_dwi.bval
│ ├── sub-LM001_ses-T1_dwi.bvec
│ ├── sub-LM001_ses-T1_dwi.json
│ └── sub-LM001_ses-T1_dwi.nii.gz
└── fmap
├── sub-LM001_ses-T1_dir-PA_epi.bval
├── sub-LM001_ses-T1_dir-PA_epi.bvec
├── sub-LM001_ses-T1_dir-PA_epi.json
└── sub-LM001_ses-T1_dir-PA_epi.nii.gz

json setup:

sub-LM001_ses-T1_dir-PA_epi.json

    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20240202",
    "Dcm2bidsVersion": "3.1.1",
    "B0FieldIdentifier": "fmap_dwi"

sub-LM001_ses-T1_dwi.json

    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20240202",
    "Dcm2bidsVersion": "3.1.1",
    "B0FieldSource": "fmap_dwi",
    "B0FieldIdentifier": "fmap_dwi"

Screenshots / relevant information:


Hi @yijun,

Qsiprep does not yet accept the B0Field method. Please use the relative path IntendedFor method instead.

Best,
Steven

Hi @Steven

Thanks for your reply.

I changed the json for fmap:

    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20240202",
    "Dcm2bidsVersion": "3.1.1",
    "IntendedFor": "dwi/sub-LM001_ses-T1_dwi.nii.gz"

However, I got the following error:

bids-validator@1.8.4

        1: [ERR] 'IntendedFor' field needs to point to an existing file. (code: 37 - INTENDED_FOR)
                ./sub-LM001/ses-T1/fmap/sub-LM001_ses-T1_dir-PA_epi.nii.gz
                        Evidence: dwi/sub-LM001_ses-T1_dwi.nii.gz

Hi @yijun,

It needs the session folder too.

Best,
Steven

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