Dear @abore and @Steven,
Thank you very much for your help
- What version of
dcm2bids
are you using? Can you also share your command?
|dcm2bids version:|3.1.1|
|Based on BIDS version:|v1.8.0|
-
Can you return the output of tree
run on your subject folder after running dcm2bids
?
Sorry, I am not sure what you mean here? I tried to find the command in the doc of pybids
but I could’nt
-
Can you share relevant JSON files from the dcm2niix
process that you are using to define your critera?
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.263,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFP",
"ProcedureStepDescription": "PRIMATES^DYNT2M",
"SoftwareVersions": "syngo MR E11",
"MRAcquisitionType": "2D",
"SeriesDescription": "se_epi_PA",
"ProtocolName": "se_epi_PA",
"ScanningSequence": "EP",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"SequenceName": "epse2d1_62",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"MOSAIC"
],
"SeriesNumber": 7,
"AcquisitionTime": "18:26:59.582500",
"AcquisitionNumber": 1,
"ImageComments": "Session:IRM_DYNT2M_PA09244_20230426_1830",
"SliceThickness": 1.25,
"SpacingBetweenSlices": 1.375,
"SAR": 0.0370679,
"EchoTime": 0.0638,
"RepetitionTime": 3.43,
"FlipAngle": 90,
"PartialFourier": 1,
"BaseResolution": 88,
"ShimSetting": [
-4617,
-3674,
4508,
498,
-533,
-4178,
-3,
-526
],
"TxRefAmp": 63.5939,
"PhaseResolution": 1,
"ReceiveCoilName": "8ChConnectorBox",
"ReceiveCoilActiveElements": "RX1-8",
"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
"WipMemBlock": "0afa0085-c433-4b23-95f7-6ce1c1e05452||Sequence: R016 ve11c/master r/e634e98; Dec 19 2017 11:22:56 by eja",
"CoilCombinationMethod": "Sum of Squares",
"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 70.4545,
"PercentSampling": 100,
"EchoTrainLength": 62,
"PhaseEncodingSteps": 62,
"AcquisitionMatrixPE": 62,
"ReconMatrixPE": 62,
"BandwidthPerPixelPhaseEncode": 17.343,
"EffectiveEchoSpacing": 0.000930002,
"DerivedVendorReportedEchoSpacing": 0.000930002,
"TotalReadoutTime": 0.0567301,
"PixelBandwidth": 1625,
"DwellTime": 3.5e-06,
"PhaseEncodingDirection": "j",
"SliceTiming": [
1.705,
0,
1.8125,
0.1075,
1.9175,
0.2125,
2.025,
0.32,
2.13,
0.425,
2.2375,
0.5325,
2.345,
0.64,
2.45,
0.745,
2.5575,
0.8525,
2.665,
0.96,
2.77,
1.065,
2.8775,
1.1725,
2.9825,
1.2775,
3.09,
1.385,
3.1975,
1.4925,
3.3025,
1.5975
],
"ImageOrientationPatientDICOM": [
1,
0,
0,
0,
-0.0139622,
-0.999903
],
"ImageOrientationText": "Cor>Tra(0.8)",
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220505",
"Dcm2bidsVersion": "3.1.1"
}
- Do you get any errors while running
dcm2bids
? Any informative log files?
2023-11-29 11:05:49.452 - INFO - dcm2niix_gen.execute | Check log file for dcm2niix output
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | SIDECAR PAIRING
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | No Pairing <- 001_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_cRX2_i00010
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | No Pairing <- 001_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_cRX4_i00006
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | No Pairing <- 001_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_cRX8_i00001
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | No Pairing <- 002_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_i00010
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | No Pairing <- 002_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_i00006
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | No Pairing <- 002_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_i00001
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | No Pairing <- 003_scans_t1_starvibe_tra_0.9mm_20230426175533
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | No Pairing <- 004_scans_EPFID_TR1700_TE18.4_32c_AP_QC_20230426175533
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | No Pairing <- 005_scans_EPFID_TR1700_TE18.4_32c_PA_QC_20230426175533
2023-11-29 11:05:49.462 - INFO - sidecar.build_acquisitions | sub-PA09244_ses-2_dir-PA_fmap <- 006_scans_se_epi_AP_20230426175533
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | sub-PA09244_ses-2_dir-AP_fmap <- 007_scans_se_epi_PA_20230426175533
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | sub-PA09244_ses-2_task-active_bold <- 008_scans_RUN01_Active_20230426175533
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | sub-PA09244_ses-2_task-active_bold <- 009_scans_RUN02_Active_20230426175533
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | No Pairing <- 010_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_cRX6_i00010
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | No Pairing <- 010_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_cRX1_i00006
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | No Pairing <- 010_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_cRX2_i00001
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | No Pairing <- 011_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_i00010
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | No Pairing <- 011_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_i00006
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | No Pairing <- 011_scans_LOCAHASTE_3_PLANS_15s_FOV154_20230426175533_i00001
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | sub-PA09244_ses-2_task-active_bold <- 012_scans_RUN03_Active_20230426175533
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | sub-PA09244_ses-2_task-active_bold <- 013_scans_RUN04_Active_20230426175533
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | No Pairing <- 014_scans_gre_field_mapping_20cpes_2.3mmiso_20230426175533_e1
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | No Pairing <- 014_scans_gre_field_mapping_20cpes_2.3mmiso_20230426175533_e2
2023-11-29 11:05:49.463 - INFO - sidecar.build_acquisitions | No Pairing <- 015_scans_gre_field_mapping_20cpes_2.3mmiso_20230426175533_e2_ph
2023-11-29 11:05:49.464 - INFO - sidecar.find_runs | sub-PA09244/ses-2/func/sub-PA09244_ses-2_task-active_bold has 4 runs
2023-11-29 11:05:49.464 - INFO - sidecar.find_runs | Adding run information to the acquisition
2023-11-29 11:05:49.464 - INFO - dcm2bids_gen.run | Moving acquisitions into BIDS folder "DynT2M_NHP/BIDS/sub-PA09244/ses-2".
2023-11-29 11:05:49.470 - INFO - dcm2bids.main | Logs saved in DynT2M_NHP/BIDS/tmp_dcm2bids/log/sub-PA09244_ses-2_20231129-110327.log
2023-11-29 11:05:49.470 - INFO - dcm2bids.main | --- dcm2bids end ---
No errors while running dcm2bids
I tried to change “custom_entities”: “map-PA” for “custom_entities”: “dir-PA” but it didn’t work.
The thing is that I didn’t managed to get any info in the doc:
https://unfmontreal.github.io/Dcm2Bids/docs/how-to/use-main-commands/
explaining why or the recommandation for using T1w instate of T1 for example.
I find it confusing that their is no error message or info in the log file. For example writting: “T1 does’nt fit the BIDS recommandations, so we ignor it” would be very useful.
But I am new in BIDS, so maybe I havn’t spotted to good documentation to correctly rename the files.
Thank you again!