Summary of What Happened
Dear community,
I was able to run dcm2bids with files that have the same series description, protocol name and series number after putting the dicom files into different source folders (fmap_run1, fmap_run2, rest_run1, rest_run2).
The program then automatically recognizes that there are two runs and added the run information to the aquisition.
SIDECAR PAIRING
INFO | sub-5489_ses-V5_magnitude1 <- 029_ses-V5_gre_field_mapping_2.5mm_20250429114159_e1
INFO | sub-5489_ses-V5_magnitude2 <- 029_ses-V5_gre_field_mapping_2.5mm_20250429114159_e2
INFO | sub-5489_ses-V5_phasediff <- 030_ses-V5_gre_field_mapping_2.5mm_20250429114159_e2_ph
INFO | sub-5489_ses-V5_task-rest_bold <- 031_ses-V5_Rest_ep2d_bold_s4_2p5mm_20250429114159
INFO | sub-5489_ses-V5_magnitude1 <- 029_ses-V5_gre_field_mapping_2.5mm_20250429121730_e1
INFO | sub-5489_ses-V5_magnitude2 <- 029_ses-V5_gre_field_mapping_2.5mm_20250429121730_e2
INFO | sub-5489_ses-V5_phasediff <- 030_ses-V5_gre_field_mapping_2.5mm_20250429121730_e2_ph
INFO | sub-5489_ses-V5_task-rest_bold <- 031_ses-V5_Rest_ep2d_bold_s4_2p5mm_20250429121730
INFO | sub-5489/ses-V5/func/sub-5489_ses-V5_task-rest_bold has 2 runs
INFO | Adding run information to the acquisition
INFO | sub-5489/ses-V5/fmap/sub-5489_ses-V5_magnitude1 has 2 runs
INFO | Adding run information to the acquisition
INFO | sub-5489/ses-V5/fmap/sub-5489_ses-V5_magnitude2 has 2 runs
INFO | Adding run information to the acquisition
INFO | sub-5489/ses-V5/fmap/sub-5489_ses-V5_phasediff has 2 runs
INFO | Adding run information to the acquisition
INFO | Moving acquisitions into BIDS folder "/server/fo2-22/data/AcEx/BIDS/new_scaffold/BIDS/sub-5489/ses-V5".
Unfortunately, when I open the meta data for the sub-5490_ses-V4_run-01_phasediff.json, both runs are listed. The same for sub-5490_ses-V4_run-02_phasediff.json
"IntendedFor": [
"bids::sub-5489/ses-V5/func/sub-5489_ses-V5_task-rest_run-01_bold.nii.gz",
"bids::sub-5489/ses-V5/func/sub-5489_ses-V5_task-rest_run-02_bold.nii.gz"
]
I could certainly order the runs as separate sessions (ses-V5pre and ses-V5post). In this case the assignment is clear. But I would like to keep the run information without editing the meta data.
Best,
Ralf
Code Used
"descriptions": [
{
"id": "task-rest",
"datatype": "func",
"suffix": "bold",
"custom_entities":"task-rest",
"criteria": {
"ProtocolName": "Rest_ep2d_bold_s4_2p5mm"
},
"sidecar_changes": {
"TaskName": "rest"
}
},
{
"datatype": "fmap",
"suffix": "phasediff",
"criteria": {
"EchoTime1": 0.00492,
"EchoTime2": 0.00738,
"ProtocolName": "gre_field_mapping_2.5mm"
},
"B0FieldIdentifier": "phasediff",
"sidecar_changes": {
"IntendedFor": [
"task-rest"
]
}
},
{
"datatype": "fmap",
"suffix": "magnitude1",
"criteria": {
"ImageType":["ORIG*", "PRIMARY", "M","ND"],
"EchoTime": 0.00492
},
"sidecar_changes": {}
},
{
"datatype": "fmap",
"suffix": "magnitude2",
"criteria": {
"ImageType":["ORIG*", "PRIMARY", "M","ND"],
"EchoTime": 0.00738
},
"sidecar_changes": {}
}
]
}
Version:
3.2.0
Environment (Docker, Singularity / Apptainer, custom installation):
apptainer
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