Hello everyone!
I ran a draft of my BIDS dataset through the BIDS validator and I got several errors. While trying to fix those, I noticed that whatever I put in my configuration files, it doesn’t change anything. For example, it indicates “error: SIDECAR_KEY_REQUIRED (TaskName)”. I updated my configuration file and made sure that the TaskName sidecar is in there. But when I check my json files after re-running dcm2bids, it still doesn’t include the TaskName. Similarly, the fieldmap json files do not include the IntendedFor information, even though I included this in the configuration file just like explained in the dcm2bids documentation. I would really appreciate it if someone could check my scripts and configuration files to see why exactly this is happening. Thank you!
dcm2bids version: 3.2.0
dcm2niix version: v1.0.20240202
CONFIGURATION FILE
{
"descriptions": [
{
"id": "id_task-RS1",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-RS1",
"criteria": {
"ProtocolName": "Mb5_55slice_RS1"
},
"sidecarChanges": {
"TaskName": "RS1"
}
},
{
"id": "id_task-training1",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-training1",
"criteria": {
"ProtocolName": "Mb5_55slice_MSL_1"
},
"sidecarChanges": {
"TaskName": "training1"
}
},
{
"id": "id_task-training2",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-training2",
"criteria": {
"ProtocolName": "Mb5_55slice_MSL_2"
},
"sidecarChanges": {
"TaskName": "training2"
}
},
{
"id": "id_task-test",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-test",
"criteria": {
"ProtocolName": "Mb5_55slice_MSL_TEST"
},
"sidecarChanges": {
"TaskName": "test"
}
},
{
"id": "id_task-RS2",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-RS2",
"criteria": {
"ProtocolName": "Mb5_55slice_RS2"
},
"sidecarChanges": {
"TaskName": "RS2"
}
},
{
"datatype": "fmap",
"suffix": "epi",
"criteria": {
"ProtocolName": "gre_field_mapping",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "NONE"],
"EchoTime": 0.00519
},
"sidecarChanges": {
"TaskName": "fmap_magn1_sess1",
"IntendedFor":[
"id_task-RS1",
"id_task-training1",
"id_task-training2",
"id_task-test",
"id_task-RS2"
]
}
},
{
"datatype": "fmap",
"suffix": "epi",
"criteria": {
"ProtocolName": "gre_field_mapping",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "NONE"],
"EchoTime": 0.00765
},
"sidecarChanges": {
"TaskName": "fmap_magn2_sess1",
"IntendedFor":[
"id_task-RS1",
"id_task-training1",
"id_task-training2",
"id_task-test",
"id_task-RS2"
]
}
},
{
"datatype": "fmap",
"suffix": "phasediff",
"criteria": {
"ProtocolName": "gre_field_mapping",
"ImageType": ["ORIGINAL", "PRIMARY", "P", "NONE", "PHASE"]
},
"sidecarChanges": {
"TaskName": "fmap_phasediff_sess1",
"IntendedFor": [
"id_task-RS1",
"id_task-training1",
"id_task-training2",
"id_task-test",
"id_task-RS2"
]
}
}
]
}
PYTHON SCRIPT (2 sessions but included configuration file of just 1)
import subprocess
# Function to run dcm2bids command
def run_dcm2bids(dicom_dir, participant, session, config_file, output_dir):
# Constructing the command
command = [
'dcm2bids', # Command to be executed
'-d', dicom_dir, # DICOM directory argument
'-p', participant, # Participant ID argument
'-s', session, # Session ID argument
'-c', config_file, # Configuration file argument
'-o', output_dir, # Output directory argument
'--auto_extract_entities',
'--force'
]
# Running the command
subprocess.run(command, check=True)
# Participant ID
participant = '101'
# List of session directories for the participant and corresponding session information
sessions = [
{
'session': 's02',
'dicom_dir': r'C:\Users\u1350546\Documents\Analysis_MRI_Data\E101\DCM\func\sess2',
'config_file': r'C:\Users\u1350546\Box\Ankes documents\Lifespan Imaging Project\Data analysis\DCM2BIDS\configuration_files\dcm2bids_config_func_sess1.json',
'output_dir': r'C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS'
},
{
'session': 's03',
'dicom_dir': r'C:\Users\u1350546\Documents\Analysis_MRI_Data\E101\DCM\func\sess3',
'config_file': r'C:\Users\u1350546\Box\Ankes documents\Lifespan Imaging Project\Data analysis\DCM2BIDS\configuration_files\dcm2bids_config_func_sess2.json',
'output_dir': r'C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS'
}
]
# Run dcm2bids for each session
for session_info in sessions:
run_dcm2bids(
dicom_dir=session_info['dicom_dir'],
participant=participant,
session=session_info['session'],
config_file=session_info['config_file'],
output_dir=session_info['output_dir']
)
TASK JSON FILE (sub-101_ses-s02_task-training1_bold.json)
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.257897,
"Manufacturer": "Siemens",
"ManufacturersModelName": "MAGNETOM Vida",
"InstitutionName": "UNIVERSITY of UTAH",
"InstitutionAddress": "Arrapeen Dr. 729,Salt Lake City,UTAH,US,84108",
"DeviceSerialNumber": "176038",
"StationName": "AWP176038",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"ProcedureStepDescription": "MRE729",
"SoftwareVersions": "syngo MR XA50",
"MRAcquisitionType": "2D",
"SeriesDescription": "Mb5_55slice_MSL_1",
"ProtocolName": "Mb5_55slice_MSL_1",
"ScanningSequence": "EP",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"PulseSequenceName": "*epfid2d1_88",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"FMRI",
"NONE"
],
"ImageTypeText": [
"ORIGINAL",
"PRIMARY",
"M",
"ND"
],
"NonlinearGradientCorrection": false,
"SeriesNumber": 8,
"AcquisitionTime": "10:13:38.577500",
"AcquisitionNumber": 1,
"SliceThickness": 2.5,
"SpacingBetweenSlices": 2.5,
"EchoTime": 0.031,
"RepetitionTime": 0.797,
"MTState": false,
"FlipAngle": 59,
"PartialFourier": 1,
"BaseResolution": 88,
"ShimSetting": [
-4270,
9543,
9392,
781,
4,
-315,
-461,
211
],
"TxRefAmp": 304.876,
"PhaseResolution": 1,
"ReceiveCoilName": "HeadNeck_64_CS",
"ReceiveCoilActiveElements": "HC3-7",
"CoilString": "HeadNeck_64_CS",
"PulseSequenceDetails": "%SiemensSeq%\\ep2d_bold",
"RefLinesPE": 21,
"CoilCombinationMethod": "Adaptive Combine",
"MultibandAccelerationFactor": 5,
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 88,
"PhaseEncodingSteps": 88,
"FrequencyEncodingSteps": 88,
"AcquisitionMatrixPE": 88,
"ReconMatrixPE": 88,
"BandwidthPerPixelPhaseEncode": 20.292,
"ParallelAcquisitionTechnique": "SMS",
"EffectiveEchoSpacing": 0.000560006,
"DerivedVendorReportedEchoSpacing": 0.000560006,
"AcquisitionDuration": 1203.7,
"TotalReadoutTime": 0.0487205,
"PixelBandwidth": 2273,
"DwellTime": 2.5e-06,
"PhaseEncodingDirection": "j-",
"SliceTiming": [
0,
0.4225,
0.07,
0.4925,
0.14,
0.565,
0.21,
0.635,
0.2825,
0.705,
0.3525,
0,
0.4225,
0.07,
0.4925,
0.14,
0.565,
0.21,
0.635,
0.2825,
0.705,
0.3525,
0,
0.4225,
0.07,
0.4925,
0.14,
0.565,
0.21,
0.635,
0.2825,
0.705,
0.3525,
0,
0.4225,
0.07,
0.4925,
0.14,
0.565,
0.21,
0.635,
0.2825,
0.705,
0.3525,
0,
0.4225,
0.07,
0.4925,
0.14,
0.565,
0.21,
0.635,
0.2825,
0.705,
0.3525
],
"ImageOrientationPatientDICOM": [
1,
0,
0,
0,
1,
0
],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"BidsGuess": [
"func",
"_acq-epfid2m5_dir-AP_run-8_bold"
],
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20240202",
"Dcm2bidsVersion": "3.2.0"
}
MAGNITUDE FIELDMAP JSON FILE (sub-101_ses-s02_dir-AP_run-02_epi)
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.257875,
"Manufacturer": "Siemens",
"ManufacturersModelName": "MAGNETOM Vida",
"InstitutionName": "UNIVERSITY of UTAH",
"InstitutionAddress": "Arrapeen Dr. 729,Salt Lake City,UTAH,US,84108",
"DeviceSerialNumber": "176038",
"StationName": "AWP176038",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"ProcedureStepDescription": "MRE729",
"SoftwareVersions": "syngo MR XA50",
"MRAcquisitionType": "2D",
"SeriesDescription": "gre_field_mapping",
"ProtocolName": "gre_field_mapping",
"ScanningSequence": "GR",
"SequenceVariant": "SP",
"PulseSequenceName": "*fm2d2r",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"NONE"
],
"ImageTypeText": [
"ORIGINAL",
"PRIMARY",
"M",
"DIS2D"
],
"NonlinearGradientCorrection": true,
"SeriesNumber": 4,
"AcquisitionTime": "10:00:24.005000",
"AcquisitionNumber": 1,
"SliceThickness": 2.5,
"SpacingBetweenSlices": 2.5,
"EchoNumber": 2,
"EchoTime": 0.00765,
"RepetitionTime": 0.752,
"MTState": false,
"FlipAngle": 90,
"PartialFourier": 1,
"BaseResolution": 88,
"ShimSetting": [
-4270,
9543,
9392,
781,
4,
-315,
-461,
211
],
"TxRefAmp": 304.876,
"PhaseResolution": 1,
"ReceiveCoilName": "HeadNeck_64_CS",
"ReceiveCoilActiveElements": "HC3-7",
"CoilString": "HeadNeck_64_CS",
"PulseSequenceDetails": "%SiemensSeq%\\gre_field_mapping",
"CoilCombinationMethod": "Sum of Squares",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"PhaseEncodingSteps": 88,
"FrequencyEncodingSteps": 88,
"AcquisitionMatrixPE": 88,
"ReconMatrixPE": 88,
"AcquisitionDuration": 131.587,
"PixelBandwidth": 434,
"DwellTime": 1.31e-05,
"PhaseEncodingDirection": "j-",
"SliceTiming": [
0,
0.3825,
0.0125,
0.395,
0.0275,
0.41,
0.04,
0.4225,
0.055,
0.4375,
0.0675,
0.45,
0.0825,
0.465,
0.095,
0.4775,
0.1075,
0.4925,
0.1225,
0.505,
0.135,
0.52,
0.15,
0.5325,
0.1625,
0.545,
0.1775,
0.56,
0.19,
0.5725,
0.205,
0.5875,
0.2175,
0.6,
0.2325,
0.615,
0.245,
0.6275,
0.26,
0.6425,
0.2725,
0.655,
0.2875,
0.67,
0.3,
0.6825,
0.3125,
0.6975,
0.3275,
0.71,
0.34,
0.725,
0.355,
0.7375,
0.3675
],
"ImageOrientationPatientDICOM": [
1,
0,
0,
0,
1,
0
],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"BidsGuess": [
"fmap",
"_acq-fm2_magnitude2"
],
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20240202",
"Dcm2bidsVersion": "3.2.0"
}
LOG OUTPUT FILE
2024-09-10 09:34:06.645 - INFO - dcm2bids.main | --- dcm2bids start ---
2024-09-10 09:34:06.645 - INFO - dcm2bids.main | Running the following command: C:\Users\u1350546\AppData\Local\anaconda3\envs\dcm2bids\Scripts\dcm2bids -d C:\Users\u1350546\Documents\Analysis_MRI_Data\E101\DCM\func\sess2 -p 101 -s s02 -c C:\Users\u1350546\Box\Ankes documents\Lifespan Imaging Project\Data analysis\DCM2BIDS\configuration_files\dcm2bids_config_func_sess1.json -o C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS --auto_extract_entities --force
2024-09-10 09:34:06.714 - INFO - dcm2bids.main | OS version: Windows-10-10.0.19042-SP0
2024-09-10 09:34:06.715 - INFO - dcm2bids.main | Python version: 3.12.4 | packaged by conda-forge | (main, Jun 17 2024, 10:04:44) [MSC v.1940 64 bit (AMD64)]
2024-09-10 09:34:06.717 - INFO - dcm2bids.main | dcm2bids version: 3.2.0
2024-09-10 09:34:06.780 - INFO - dcm2bids.main | dcm2niix version: v1.0.20240202
2024-09-10 09:34:06.780 - INFO - dcm2bids.main | Checking for software update
2024-09-10 09:34:07.393 - INFO - tools.check_latest | Currently using the latest version of dcm2bids.
2024-09-10 09:34:07.663 - INFO - tools.check_latest | Currently using the latest version of dcm2niix.
2024-09-10 09:34:07.664 - INFO - dcm2bids.main | participant: sub-101
2024-09-10 09:34:07.671 - INFO - dcm2bids.main | session: ses-s02
2024-09-10 09:34:07.679 - INFO - dcm2bids.main | config: C:\Users\u1350546\Box\Ankes documents\Lifespan Imaging Project\Data analysis\DCM2BIDS\configuration_files\dcm2bids_config_func_sess1.json
2024-09-10 09:34:07.679 - INFO - dcm2bids.main | BIDS directory: C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS
2024-09-10 09:34:07.680 - INFO - dcm2bids.main | Auto extract entities: True
2024-09-10 09:34:07.680 - INFO - dcm2bids.main | Reorder entities: True
2024-09-10 09:34:07.680 - INFO - dcm2bids.main | Validate BIDS: False
2024-09-10 09:34:07.696 - INFO - utils.run_shell_command | Running: dcm2niix -b y -ba y -z y -f %3s_%f_%p_%t -o C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\sub-101_ses-s02 C:\Users\u1350546\Documents\Analysis_MRI_Data\E101\DCM\func\sess2
2024-09-10 09:41:10.391 - DEBUG - dcm2niix_gen.execute |
Chris Rorden's dcm2niiX version v1.0.20240202 MSC1929 (64-bit Windows)
Found 2483 DICOM file(s)
CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range 0..3825, TR=797 ms)
Convert 375 DICOM as C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\sub-101_ses-s02\014_sess2_Mb5_55slice_RS2_20240719095640 (88x88x55x375)
CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range 0..3825, TR=797 ms)
Convert 770 DICOM as C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\sub-101_ses-s02\010_sess2_Mb5_55slice_MSL_2_20240719095640 (88x88x55x770)
CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range 0..3825, TR=797 ms)
Convert 375 DICOM as C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\sub-101_ses-s02\006_sess2_Mb5_55slice_RS1_20240719095640 (88x88x55x375)
CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range 0..3825, TR=797 ms)
Convert 807 DICOM as C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\sub-101_ses-s02\008_sess2_Mb5_55slice_MSL_1_20240719095640 (88x88x55x807)
CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range 0..3825, TR=797 ms)
Convert 153 DICOM as C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\sub-101_ses-s02\012_sess2_Mb5_55slice_MSL_TEST_20240719095640 (88x88x55x153)
Slices not stacked: echo varies (TE 5.19, 7.65; echo 1, 2). Use 'merge 2D slices' option to force stacking
Convert 1 DICOM as C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\sub-101_ses-s02\004_sess2_gre_field_mapping_20240719095640_e1 (88x88x55x1)
CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range 755..1492.5, TR=752 ms)
Convert 1 DICOM as C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\sub-101_ses-s02\004_sess2_gre_field_mapping_20240719095640_e2 (88x88x55x1)
CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range 755..1492.5, TR=752 ms)
Convert 1 DICOM as C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\sub-101_ses-s02\005_sess2_gre_field_mapping_20240719095640_e2_ph (88x88x55x1)
Conversion required 422.669006 seconds.
2024-09-10 09:41:10.391 - INFO - dcm2niix_gen.execute | Check log file for dcm2niix output
2024-09-10 09:41:10.398 - INFO - sidecar.build_acquisitions | SIDECAR PAIRING
2024-09-10 09:41:10.399 - INFO - sidecar.build_acquisitions | sub-101_ses-s02_dir-AP_epi <- 004_sess2_gre_field_mapping_20240719095640_e1
2024-09-10 09:41:10.400 - INFO - sidecar.build_acquisitions | sub-101_ses-s02_dir-AP_epi <- 004_sess2_gre_field_mapping_20240719095640_e2
2024-09-10 09:41:10.400 - INFO - sidecar.build_acquisitions | sub-101_ses-s02_phasediff <- 005_sess2_gre_field_mapping_20240719095640_e2_ph
2024-09-10 09:41:10.401 - INFO - sidecar.build_acquisitions | sub-101_ses-s02_task-RS1_bold <- 006_sess2_Mb5_55slice_RS1_20240719095640
2024-09-10 09:41:10.401 - INFO - sidecar.build_acquisitions | sub-101_ses-s02_task-training1_bold <- 008_sess2_Mb5_55slice_MSL_1_20240719095640
2024-09-10 09:41:10.402 - INFO - sidecar.build_acquisitions | sub-101_ses-s02_task-training2_bold <- 010_sess2_Mb5_55slice_MSL_2_20240719095640
2024-09-10 09:41:10.402 - INFO - sidecar.build_acquisitions | sub-101_ses-s02_task-test_bold <- 012_sess2_Mb5_55slice_MSL_TEST_20240719095640
2024-09-10 09:41:10.402 - INFO - sidecar.build_acquisitions | sub-101_ses-s02_task-RS2_bold <- 014_sess2_Mb5_55slice_RS2_20240719095640
2024-09-10 09:41:10.403 - INFO - sidecar.find_runs | sub-101\ses-s02\fmap\sub-101_ses-s02_dir-AP_epi has 2 runs
2024-09-10 09:41:10.403 - INFO - sidecar.find_runs | Adding run information to the acquisition
2024-09-10 09:41:10.404 - INFO - dcm2bids_gen.run | Moving acquisitions into BIDS folder "C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\sub-101\ses-s02".
2024-09-10 09:41:10.432 - INFO - dcm2bids.main | Logs saved in C:\Users\u1350546\Documents\Analysis_MRI_Data\OfflineBrain_BIDS\tmp_dcm2bids\log\sub-101_ses-s02_20240910-093406.log
2024-09-10 09:41:10.432 - INFO - dcm2bids.main | --- dcm2bids end ---
