Dcm2bids Warning: {'task'} have not been found for datatype 'func' and suffix 'bold'

Software Support
1

Hello everyone!

I’m trying to figure out how to convert my fMRI DCM files to BIDS and I’m getting the following warning: {‘task’} have not been found for datatype ‘func’ and suffix ‘bold’. I know that others have posted about this, but I do have the custom_entities in here and it’s still not working. Below you can find the content of my configuration file. I would appreciate any tips on how to fix this! :slight_smile:

{
  "descriptions": [
    {
      "datatype": "func",
      "suffix": "bold",
      "custom_entities": "task-retest",
      "criteria": {
        "ProtocolName": "Mb5_55slice_RETEST"
      },
      "sidecarChanges": {
	"TaskName": "task-retest"
      }
    }               
   ]
  }
2

Hi @ankevr97 and welcome to neurostars!

It is hard to help without seeing your full log, an example JSON for a BOLD file, seeing your command, and knowing what version of dcm2bids you are using. Please provide that information for assistance. When providing terminal text (e.g., the command, json contents, or output log), please format it as code so it looks nice

like this (use the </> button in the text editor).

You can see I edited that for your JSON in your original post.

Best,
Steven

3

Log
Log1899×873 276 KB

(dcm2bids) C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR>dcm2bids -d C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\Sub01\Sess01\func -p ID01 -s s01 -c C:\ Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\dcm2bids_config_test.json --auto_extract_entities --force
INFO
dcm2bids start
INFO | Running the following command: C:\Users\u1350546\AppData\Local\anaconda3\envs\dcm2bids\Scripts\dcm2bids -d C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\ Sub01\Sess01\func -p ID01 -s s01 -c C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\dcm2bids_config_test.json --auto_extract_entities --force INFO | OS version: Windows-10-10.0.19042-SPO
INFO
INFO
INFO
INFO
WARNING
WARNING
INFO
INFO
INFO
INFO
INFO
INFO INFO
INFO
| Python version: 3.12.4 | packaged by Anaconda, Inc. | (main, Jun 18 2024, 15:03:56) [MSC v.1929 64 bit (AMD64)] dcm2bids version: 3.1.1
dcm2niix version: v1.0.20240202
Checking for software update
A newer version exists for dcm2bids: 3.2.0
You should update it -> https://github.com/UNFmontreal/Dcm2Bids.
Currently using the latest version of dcm2niix.
participant: sub-ID01
session: ses-s01
config: C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\dcm2bids_config_test.json
BIDS directory: C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR
Auto extract entities: True Validate BIDS: False
| Running: dcm2niix -b y -ba y -z y -f %3s_%f_%p_%t -o C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\tmp_dcm2bids\sub-ID01_ses-s01 C:\Users\u1350546\Docume nts\Analysis_MRI_Data\Test_AVR\Sub01\Sess01\func
INFO | Check log file for dcm2niix output
INFO
WARNING | SIDECAR PAIRING
{'task'} have not been found for datatype 'func' and suffix 'bold'.
sub-ID01_ses-s01_task-retest_bold <- 008_func_Mb5_55slice_RETEST_20230608152748
Moving acquisitions into BIDS folder "C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\sub-ID01\ses-s01".
'C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\sub-ID01\ses-s01\func\sub-ID01_ses-s01_task-retest_bold.nii.gz' already exists
Use --clobber option to overwrite
'C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\sub-ID01\ses-s01\func\sub-ID01_ses-s01_task-retest_bold.json' already exists
Use --clobber option to overwrite
Logs saved in C:\Users\u1350546\Documents\Analysis_MRI_Data\Test_AVR\tmp_dcm2bids \log\sub-ID01_ses-s01_20240731-130935.log dcm2bids end
4 
{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 123.258107,
    "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",
    "SoftwareVersions": "syngo MR XA50",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "Mb5_55slice_RETEST",
    "ProtocolName": "Mb5_55slice_RETEST",
    "ScanningSequence": "EP",
    "SequenceVariant": "SK",
    "ScanOptions": "FS",
    "PulseSequenceName": "*epfid2d1_88",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "FMRI",
        "NONE"
    ],
    "ImageTypeText": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND"
    ],
    "NonlinearGradientCorrection": false,
    "SeriesNumber": 8,
    "AcquisitionTime": "15:49:46.160000",
    "AcquisitionNumber": 1,
    "SliceThickness": 2.5,
    "SpacingBetweenSlices": 2.5,
    "EchoTime": 0.031,
    "RepetitionTime": 0.797,
    "MTState": false,
    "FlipAngle": 59,
    "PartialFourier": 1,
    "BaseResolution": 88,
    "ShimSetting": [
        -4231,
        9625,
        9377,
        954,
        57,
        -205,
        -509,
        137
    ],
    "TxRefAmp": 318.468,
    "PhaseResolution": 1,
    "ReceiveCoilName": "HeadNeck_64_CS",
    "ReceiveCoilActiveElements": "HC1-7",
    "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": 1203.71,
    "TotalReadoutTime": 0.0487205,
    "PixelBandwidth": 2273,
    "DwellTime": 2.5e-06,
    "PhaseEncodingDirection": "j",
    "SliceTiming": [
        0,
        0.425,
        0.07,
        0.495,
        0.1425,
        0.565,
        0.2125,
        0.635,
        0.2825,
        0.7075,
        0.3525,
        0,
        0.425,
        0.07,
        0.495,
        0.1425,
        0.565,
        0.2125,
        0.635,
        0.2825,
        0.7075,
        0.3525,
        0,
        0.425,
        0.07,
        0.495,
        0.1425,
        0.565,
        0.2125,
        0.635,
        0.2825,
        0.7075,
        0.3525,
        0,
        0.425,
        0.07,
        0.495,
        0.1425,
        0.565,
        0.2125,
        0.635,
        0.2825,
        0.7075,
        0.3525,
        0,
        0.425,
        0.07,
        0.495,
        0.1425,
        0.565,
        0.2125,
        0.635,
        0.2825,
        0.7075,
        0.3525
    ],
    "ImageOrientationPatientDICOM": [
        1,
        0,
        0,
        0,
        1,
        0
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "BidsGuess": [
        "func",
        "_acq-epfid2m5_dir-PA_run-8_bold"
    ],
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20240202",
    "Dcm2bidsVersion": "3.1.1"
}
5

Hi @ankevr97,

Please update to 3.2.0 and try again.

Best,
Steven

6

That worked, thank you!

Quick follow-up: I can just use dcm2bids on a folder with 3D files instead of a 4D files, right?

7

Hi @ankevr97,

Can you explain what you mean by this? Dcm2bids converts 3D (e.g. T1) and 4D (e.g., bold timeseries) data, but I’m not sure that’s what you’re asking.

Best,
Steven

8

Sorry for the confusion! Instead of a single 4D bold timeseries file, our Siemens scanner gives us a bunch of 3D files for one run, so a 3D DCM file for each TR. Everything on the Dcm2bids website is written about 4D files, so I was wondering if that’s an issue.

9

What does the dcm2niix output look like?