1005 newborn (Stanford) Fails BIDS conversion

[scott-huberty]

Command:

First I mounted the dcm2bids image:

docker run --rm -it --entrypoint /bin/bash -v /Users/scotterik/devel/scratch/Babies_newborn_raw/sourcedata:/dicoms -v /Users/scotterik/devel/scratch/Babies_newborn_raw/bids:/bids -v ~/devel/scratch/Babies_newborn_raw/dcm2bids_config.json:/config.json:ro unfmontreal/dcm2bids

Then I ran this command:

dcm2bids -o /bids -d /dicoms -p 1005 -c /config.json

Error:

INFO    | --- dcm2bids start ---
INFO    | Running the following command: /venv/bin/dcm2bids -o /bids -d /dicoms -p 1005 -c /config.json
INFO    | OS version: Linux-6.10.14-linuxkit-x86_64-with-glibc2.36
INFO    | Python version: 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
INFO    | dcm2bids version: 3.2.0
INFO    | dcm2niix version: v1.0.20240202
INFO    | Checking for software update
INFO    | Currently using the latest version of dcm2bids.
WARNING | A newer version exists for dcm2niix: v1.0.20241211
WARNING | You should update it -> https://github.com/rordenlab/dcm2niix.
INFO    | participant: sub-1005
INFO    | config: /config.json
INFO    | BIDS directory: /bids
INFO    | Auto extract entities: False
INFO    | Reorder entities: True
INFO    | Validate BIDS: False

INFO    | Running: dcm2niix -b y -ba y -z y -f %3s_%f_%p_%t -o /bids/tmp_dcm2bids/sub-1005 /dicoms
INFO    | Log from dcm2niix execution
WARNING | Chris Rorden's dcm2niiX version v1.0.20240202  (JP2:OpenJPEG) (JP-LS:CharLS) GCC8.4.0 x86-64 (64-bit Linux)
Found 7510 DICOM file(s)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/007_dicoms_Gotlib_BABIES_L-6month_0_20181212203020 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_C_BABIES_newborn_20190423213712 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20171203221843 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_06_20171024221336 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_01_20190223214101 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_06_20170924172843 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20180826202801 (256x256x204x1)
Convert 168 DICOM as /bids/tmp_dcm2bids/sub-1005/007_dicoms_Gotlib_BABIES_newborn_08_20180716211053 (256x256x168x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_C_BABIES_newborn_20190610223213 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20180824193814 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/012_dicoms_Gotlib_BABIES_newborn_06_20170705203834 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_01_20190215203139 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20180119220701 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_L-6month_0_20190220200045 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/008_dicoms_Gotlib_BABIES_newborn_08_20180905201421 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_C_BABIES_newborn_20190726204858 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/006_dicoms_Gotlib_BABIES_newborn_08_20180518195137 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/012_dicoms_Gotlib_BABIES_newborn_06_20170725195912 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20180204225724 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20180129215534 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20180403205753 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_01_20190316204528 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20181102193503 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20180912232904 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/004_dicoms_Gotlib_BABIES_newborn_08_20180806212428 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20171111194644 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/005_dicoms_Gotlib_BABIES_newborn_01_20190311202517 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20180319222622 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_06_20171002223456 (256x256x204x1)
DICOM images may be missing, expected 204 spatial locations per volume, but found 202 slices.
Warning: Instance Number (0020,0013) order is not spatial.
Warning: Interslice distance varies in this volume (incompatible with NIfTI format).
Convert 202 DICOM as /bids/tmp_dcm2bids/sub-1005/004_dicoms_Gotlib_BABIES_newborn_05_20170602210230 (256x256x202x1)
Warning: Unable to rotate 3D volume: slices not equidistant: 0.799995 != 1.6
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20171129195209 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/004_dicoms_Gotlib_BABIES_newborn_08_20180601192426 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20180124203642 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_08_20171118223959 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/005_dicoms_Gotlib_C_BABIES_newborn_20190516193314 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_01_20190117205109 (256x256x204x1)
Convert 204 DICOM as /bids/tmp_dcm2bids/sub-1005/004_dicoms_Gotlib_BABIES_newborn_08_20181013191805 (256x256x204x1)
Conversion required 102.579698 seconds (81.708641 for core code).

INFO    | SIDECAR PAIRING
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_06_20170924172843
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20181102193503
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20180824193814
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20171111194644
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20171129195209
INFO    | No Pairing  <-  004_dicoms_Gotlib_BABIES_newborn_08_20181013191805
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_L-6month_0_20190220200045
INFO    | No Pairing  <-  004_dicoms_Gotlib_BABIES_newborn_08_20180601192426
INFO    | No Pairing  <-  005_dicoms_Gotlib_C_BABIES_newborn_20190516193314
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20180826202801
INFO    | No Pairing  <-  005_dicoms_Gotlib_BABIES_newborn_01_20190311202517
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_01_20190215203139
INFO    | No Pairing  <-  012_dicoms_Gotlib_BABIES_newborn_06_20170725195912
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20180124203642
INFO    | No Pairing  <-  006_dicoms_Gotlib_BABIES_newborn_08_20180518195137
INFO    | No Pairing  <-  003_dicoms_Gotlib_C_BABIES_newborn_20190726204858
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_01_20190117205109
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20180403205753
INFO    | No Pairing  <-  012_dicoms_Gotlib_BABIES_newborn_06_20170705203834
INFO    | No Pairing  <-  007_dicoms_Gotlib_BABIES_newborn_08_20180716211053
INFO    | No Pairing  <-  004_dicoms_Gotlib_BABIES_newborn_08_20180806212428
INFO    | No Pairing  <-  004_dicoms_Gotlib_BABIES_newborn_05_20170602210230
INFO    | No Pairing  <-  003_dicoms_Gotlib_C_BABIES_newborn_20190423213712
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_01_20190223214101
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20180129215534
INFO    | No Pairing  <-  008_dicoms_Gotlib_BABIES_newborn_08_20180905201421
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20180119220701
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_06_20171024221336
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20171203221843
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20180319222622
INFO    | No Pairing  <-  003_dicoms_Gotlib_C_BABIES_newborn_20190610223213
INFO    | No Pairing  <-  007_dicoms_Gotlib_BABIES_L-6month_0_20181212203020
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_01_20190316204528
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_06_20171002223456
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20171118223959
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20180204225724
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_08_20180912232904
WARNING | NO PAIRING WAS FOUND. BIDS FOLDER "/BIDS/SUB-1005" WON'T BE CREATED. CHECK YOUR CONFIG FILE.

INFO    | Logs saved in /bids/tmp_dcm2bids/log/sub-1005_20250309-174541.log
INFO    | --- dcm2bids end ---

Config:

{
    "descriptions": [
      {
        "datatype": "anat",
        "suffix": "T2w",
        "criteria": {
          "SeriesDescription": "*T2*",
          "EchoTime": 0.1
        },
        "sidecar_changes": {
          "ProtocolName": "T2"
        }
      }
    ]
  }

Log:

sub-1005_20250309-174541.log

[scott-huberty]

Here is the JSON file for /Users/scotterik/devel/scratch/Babies_newborn_raw/bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_06_20170924172843.json , which dcm2bids complains about i.e.

INFO    | SIDECAR PAIRING
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_newborn_06_20170924172843

{
	"Modality": "MR",
	"MagneticFieldStrength": 3,
	"ImagingFrequency": 127.765055,
	"Manufacturer": "GE",
	"ManufacturersModelName": "DISCOVERY MR750",
	"InstitutionName": "Stanford Lucas Center",
	"DeviceSerialNumber": "0000415723SCHMR2",
	"StationName": "No3",
	"PatientPosition": "HFS",
	"ProcedureStepDescription": "Cube",
	"SoftwareVersions": "25\\LX\\MR Software release:DV25.0_R02_1549.b",
	"MRAcquisitionType": "3D",
	"SeriesDescription": "T2w_0.8mm_sag",
	"ProtocolName": "Gotlib_BABIES_newborn_06",
	"ScanningSequence": "SE",
	"SequenceVariant": "SK",
	"ScanOptions": "EDR_GEMS\\ACC_GEMS",
	"PulseSequenceName": "Cube",
	"ImageType": ["ORIGINAL", "PRIMARY", "OTHER"],
	"SeriesNumber": 3,
	"AcquisitionTime": "17:29:41.000000",
	"AcquisitionNumber": 1,
	"SliceThickness": 0.8,
	"SpacingBetweenSlices": 0.8,
	"SAR": 0.798367,
	"EchoTime": 0.089947,
	"RepetitionTime": 2.5,
	"FlipAngle": 90,
	"ShimSetting": [
		-2,
		3,
		-28	],
	"PrescanReuseString": "TG/s1,CF/s1,AS/s1",
	"CoilString": "RM:Nova32ch",
	"PercentPhaseFOV": 100,
	"PercentSampling": 100,
	"EchoTrainLength": 120,
	"AcquisitionMatrixPE": 256,
	"ReconMatrixPE": 256,
	"ParallelReductionFactorInPlane": 2,
	"ParallelReductionFactorOutOfPlane": 2,
	"PixelBandwidth": 488.281,
	"PhaseEncodingAxis": "i",
	"ImageOrientationPatientDICOM": [
		-0,
		1,
		0,
		-0,
		-0,
		-1	],
	"InPlanePhaseEncodingDirectionDICOM": "ROW",
	"BidsGuess": ["anat","_acq-3DFSEp2_run-3_T2w"],
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20240202"
}

And yes there is an associated nifti file: /Users/scotterik/devel/scratch/Babies_newborn_raw/bids/tmp_dcm2bids/sub-1005/003_dicoms_Gotlib_BABIES_newborn_06_20170924172843.nii.gz

ls -1 bids/tmp_dcm2bids/sub-1005

003_dicoms_Gotlib_BABIES_L-6month_0_20190220200045.json
003_dicoms_Gotlib_BABIES_L-6month_0_20190220200045.nii.gz
003_dicoms_Gotlib_BABIES_newborn_01_20190117205109.json
003_dicoms_Gotlib_BABIES_newborn_01_20190117205109.nii.gz
003_dicoms_Gotlib_BABIES_newborn_01_20190215203139.json
003_dicoms_Gotlib_BABIES_newborn_01_20190215203139.nii.gz
003_dicoms_Gotlib_BABIES_newborn_01_20190223214101.json
003_dicoms_Gotlib_BABIES_newborn_01_20190223214101.nii.gz
003_dicoms_Gotlib_BABIES_newborn_01_20190316204528.json
003_dicoms_Gotlib_BABIES_newborn_01_20190316204528.nii.gz
003_dicoms_Gotlib_BABIES_newborn_06_20170924172843.json
003_dicoms_Gotlib_BABIES_newborn_06_20170924172843.nii.gz
003_dicoms_Gotlib_BABIES_newborn_06_20171002223456.json
003_dicoms_Gotlib_BABIES_newborn_06_20171002223456.nii.gz
003_dicoms_Gotlib_BABIES_newborn_06_20171024221336.json
003_dicoms_Gotlib_BABIES_newborn_06_20171024221336.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20171111194644.json
003_dicoms_Gotlib_BABIES_newborn_08_20171111194644.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20171118223959.json
003_dicoms_Gotlib_BABIES_newborn_08_20171118223959.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20171129195209.json
003_dicoms_Gotlib_BABIES_newborn_08_20171129195209.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20171203221843.json
003_dicoms_Gotlib_BABIES_newborn_08_20171203221843.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20180119220701.json
003_dicoms_Gotlib_BABIES_newborn_08_20180119220701.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20180124203642.json
003_dicoms_Gotlib_BABIES_newborn_08_20180124203642.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20180129215534.json
003_dicoms_Gotlib_BABIES_newborn_08_20180129215534.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20180204225724.json
003_dicoms_Gotlib_BABIES_newborn_08_20180204225724.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20180319222622.json
003_dicoms_Gotlib_BABIES_newborn_08_20180319222622.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20180403205753.json
003_dicoms_Gotlib_BABIES_newborn_08_20180403205753.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20180824193814.json
003_dicoms_Gotlib_BABIES_newborn_08_20180824193814.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20180826202801.json
003_dicoms_Gotlib_BABIES_newborn_08_20180826202801.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20180912232904.json
003_dicoms_Gotlib_BABIES_newborn_08_20180912232904.nii.gz
003_dicoms_Gotlib_BABIES_newborn_08_20181102193503.json
003_dicoms_Gotlib_BABIES_newborn_08_20181102193503.nii.gz
003_dicoms_Gotlib_C_BABIES_newborn_20190423213712.json
003_dicoms_Gotlib_C_BABIES_newborn_20190423213712.nii.gz
003_dicoms_Gotlib_C_BABIES_newborn_20190610223213.json
003_dicoms_Gotlib_C_BABIES_newborn_20190610223213.nii.gz
003_dicoms_Gotlib_C_BABIES_newborn_20190726204858.json
003_dicoms_Gotlib_C_BABIES_newborn_20190726204858.nii.gz
004_dicoms_Gotlib_BABIES_newborn_05_20170602210230.json
004_dicoms_Gotlib_BABIES_newborn_05_20170602210230.nii.gz
004_dicoms_Gotlib_BABIES_newborn_05_20170602210230_Eq_1.nii.gz
004_dicoms_Gotlib_BABIES_newborn_08_20180601192426.json
004_dicoms_Gotlib_BABIES_newborn_08_20180601192426.nii.gz
004_dicoms_Gotlib_BABIES_newborn_08_20180806212428.json
004_dicoms_Gotlib_BABIES_newborn_08_20180806212428.nii.gz
004_dicoms_Gotlib_BABIES_newborn_08_20181013191805.json
004_dicoms_Gotlib_BABIES_newborn_08_20181013191805.nii.gz
005_dicoms_Gotlib_BABIES_newborn_01_20190311202517.json
005_dicoms_Gotlib_BABIES_newborn_01_20190311202517.nii.gz
005_dicoms_Gotlib_C_BABIES_newborn_20190516193314.json
005_dicoms_Gotlib_C_BABIES_newborn_20190516193314.nii.gz
006_dicoms_Gotlib_BABIES_newborn_08_20180518195137.json
006_dicoms_Gotlib_BABIES_newborn_08_20180518195137.nii.gz
007_dicoms_Gotlib_BABIES_L-6month_0_20181212203020.json
007_dicoms_Gotlib_BABIES_L-6month_0_20181212203020.nii.gz
007_dicoms_Gotlib_BABIES_newborn_08_20180716211053.json
007_dicoms_Gotlib_BABIES_newborn_08_20180716211053.nii.gz
008_dicoms_Gotlib_BABIES_newborn_08_20180905201421.json
008_dicoms_Gotlib_BABIES_newborn_08_20180905201421.nii.gz
012_dicoms_Gotlib_BABIES_newborn_06_20170705203834.json
012_dicoms_Gotlib_BABIES_newborn_06_20170705203834.nii.gz
012_dicoms_Gotlib_BABIES_newborn_06_20170725195912.json
012_dicoms_Gotlib_BABIES_newborn_06_20170725195912.nii.gz

[scott-huberty]

One "smell" here is that the dcm2bids log is reporting on files from a 6-month timepoint, even though this should be a newborn file. i.e:

INFO    | No Pairing  <-  007_dicoms_Gotlib_BABIES_L-6month_0_20181212203020
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_L-6month_0_20190220200045

Either Babies_newborn_raw/sourcedata/1005/t2w_dicoms/ contains dicoms for the 6-month visit (which it shouldn't), or dcm2bids is pulling the wrong subjects dicoms.

[scott-huberty]

@yanbin-niu I think the issue is this field in the config file I am using:

          "EchoTime": 0.1

See UNFmontreal/Dcm2Bids#331

But I'm still concerned about my comment above. We can chat about that on Thursday.

[SamGuay]

Hi again. As mentioned previously, here's a couple of things and question to help you out.

@yanbin-niu I think the issue is this field in the config file I am using:

      "EchoTime": 0.1

I confirm that's the reason there is no match, there is no image with that specific echo time. Refer to my answer in the discussion you've opened on dcm2bids repo.

One "smell" here is that the dcm2bids log is reporting on files from a 6-month timepoint, even though this should be a newborn file. i.e:

INFO    | No Pairing  <-  007_dicoms_Gotlib_BABIES_L-6month_0_20181212203020
INFO    | No Pairing  <-  003_dicoms_Gotlib_BABIES_L-6month_0_20190220200045

Either Babies_newborn_raw/sourcedata/1005/t2w_dicoms/ contains dicoms for the 6-month visit (which it shouldn't), or dcm2bids is pulling the wrong subjects dicoms.

So it appears you are running all these commands from within a docker container as in your first post. In you docker command, you mount the volume -v /Users/scotterik/devel/scratch/Babies_newborn_raw/sourcedata:/dicoms. Does it contain only the data for one participant or many? 7510 DICOM files feels a lot for one participant, but maybe it was a very long protocol! If you suspect there are many participants inside the same directory that you mount (which "smells" like it here), this could become problematic. When you run dcm2bids for -p 1005 for example, dcm2bids finds all the DICOMS in the -d dicoms dir and convert all of them into nifti in the tmp_dcm2bids/sub-1005 directory regardless of the provenance of the dicoms (ie, whether it is the same participant or not). This is also true for a single participant with multiple sessions, which seems the case for you as you mention the 6-month timepoint. Each session should be ran with an independent dcm2bids execution. You'd then need the -s option.

It is a bit hard to help your further without knowing more but I think this should be a good start resolving your issue!

Edit: I just saw that you mention Babies_newborn_raw/sourcedata/1005/t2w_dicoms/ so you probably want to make sure that you specify at least -d /dicoms/1005 if you wanna convert many files for -p 1005 or -d /dicoms/1005/t2w_dicoms to select only the dicoms within that dir. Hope that clarifies it.

[scott-huberty]

Thanks @SamGuay ! See my response over at UNFmontreal/Dcm2Bids#330 -

Indeed I misunderstood the API, and passed -d /path/to/sourcedata where sourcedata contained a sub-directory for every participant!