Dear NeuroStars community,
When running the dcm2bids (version 3.2.0) command, I seem to incorrectly assign my fmaps to the respective “inteded for” images. I cannot figure out why the IDs cannot be matched.
Any help would me much appreciated!
Thanks so much,
Sabine
Command used
docker run --rm -it \
-v ${SOURCEDATA_DIR}/GIDEON_sub-PA1_b20000107:/dicoms:ro \
-v ${RAWDATA_DIR}:/bids \
unfmontreal/dcm2bids:${VERSION} --auto_extract_entities --bids_validate \
-o /bids -d /dicoms -c /bids/code/dcm2bids_config.json -p PA1
Relevant Log outputs
WARNING | No id found for 'IntendedFor' value 'id_education'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_magnitude1.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_cloudy'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_magnitude1.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_unverbesserlich'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_magnitude1.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_education'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_magnitude2.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_cloudy'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_magnitude2.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_unverbesserlich'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_magnitude2.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_education'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_phasediff.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_cloudy'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_phasediff.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_unverbesserlich'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_phasediff.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_dwi'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_dir-PA_epi.json' with this id.
WARNING | No id found for 'IntendedFor' value 'id_dwi'.
WARNING | No sidecar changes for field 'IntendedFor' will be made for json file 'sub-PA1_dir-AP_epi.json' with this id.
My dcm2bids config file:
{
"descriptions": [
{
"id": "id_T1w",
"datatype": "anat",
"suffix": "T1w",
"criteria": {
"SeriesDescription": "ABCD_T1w_MPR_vNav",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"NORM"
]
}
},
{
"id": "id_education",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-education",
"criteria": {
"SeriesDescription": "ABCD_fMRI_edu"
},
"sidecar_changes": {
"TaskName": "education"
}
},
{
"id": "id_cloudy",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-partlycloudy",
"criteria": {
"SeriesDescription": "ABCD_fMRI_cloudy"
},
"sidecar_changes": {
"TaskName": "partlycloudy"
}
},
{
"id": "id_unverbesserlich",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-despicableme",
"criteria": {
"SeriesDescription": "ABCD_fMRI_unverbesserlich"
},
"sidecar_changes": {
"TaskName": "despicableme"
}
},
{
"id": "id_dwi",
"datatype": "dwi",
"suffix": "dwi",
"criteria": {
"SeriesDescription": "ABCD_dMRI"
}
},
{
"id": "id_fmap_magn1",
"datatype": "fmap",
"suffix": "magnitude1",
"modalityLabel": "magnitude1",
"criteria": {
"SeriesDescription": "gre_field_mapping_2.4mm",
"EchoTime": 0.00492
},
"sidecar_changes": {
"IntendedFor": [
"id_education",
"id_cloudy",
"id_unverbesserlich"
]
}
},
{
"id": "id_fmap_magn2",
"datatype": "fmap",
"suffix": "magnitude2",
"modalityLabel": "magnitude2",
"criteria": {
"SeriesDescription": "gre_field_mapping_2.4mm",
"EchoTime": 0.00738,
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND"
]
},
"sidecar_changes": {
"IntendedFor": [
"id_education",
"id_cloudy",
"id_unverbesserlich"
]
}
},
{
"id": "id_fmap_phasediff",
"datatype": "fmap",
"suffix": "phasediff",
"modalityLabel": "phasediff",
"criteria": {
"SeriesDescription": "gre_field_mapping_2.4mm",
"EchoTime1": 0.00492,
"EchoTime2": 0.00738,
"ImageType": [
"ORIGINAL",
"PRIMARY",
"P",
"ND",
"PHASE"
]
},
"sidecar_changes": {
"IntendedFor": [
"id_education",
"id_cloudy",
"id_unverbesserlich"
]
}
},
{
"id": "id_topup_AP",
"datatype": "fmap",
"suffix": "epi",
"custom_entities": "dir-AP",
"criteria": {
"SeriesDescription": "ABCD_dMRI_DistortionMap_AP",
"PhaseEncodingDirection": "j-"
},
"sidecar_changes": {
"IntendedFor": "id_dwi"
}
},
{
"id": "id_topup_PA",
"datatype": "fmap",
"suffix": "epi",
"custom_entities": "dir-PA",
"criteria": {
"SeriesDescription": "ABCD_dMRI_DistortionMap_PA",
"PhaseEncodingDirection": "j"
},
"sidecar_changes": {
"IntendedFor": "id_dwi"
}
}
]
}
