qsiprep: Exception: Gradients or original files don't match. File a bug report!

Hi! I’m getting this error when running qsiprep 0.16.1 on my data. The two DWI sequences have 45 volumes each, one is AP and the other PA direction. There are no specific fmaps, and there are 2 T1ws being averaged. I was hoping to use TOPUP/PEPOLAR for SDC, so I’m wondering if there isn’t anything weird in the DWI JSONs that’d be causing issues when combining the data down the road?

Here’s my call to qsiprep:

qsiprep ${TMPDIR}/BIDS/ ${tmp_out_dir} participant \
    --participant_label sub-${s} -w ${wrk_dir} \
    --notrack --nthreads $SLURM_CPUS_PER_TASK \
    --mem_mb $(( SLURM_MEM_PER_NODE - 2048 )) \
    --stop-on-first-crash \
    --unringing-method mrdegibbs \
    --output-resolution 1.2 \
    --template MNI152NLin2009cAsym \
    --distortion-group-merge average \
    --fs-license-file /usr/local/apps/freesurfer/license.txt

Here’s how one of the DWI jsons look like: (the other one is similar, but PhaseEncodingDirection: j-)

(dcm2niix) [sudregp@ncrshell01 sub-test4]$ cat ses-baseline/dwi/sub-test4_ses-baseline_dir-AP_run-1_dwi.json 
{
  "Modality": "MR",
  "MagneticFieldStrength": 3,
  "ImagingFrequency": 127.824,
  "Manufacturer": "GE",
  "InternalPulseSequenceName": "EPI2",
  "ManufacturersModelName": "DISCOVERY MR750",
  "InstitutionName": "NIH FMRIF",
  "DeviceSerialNumber": "000301496MR3T5MR",
  "StationName": "fmrif3ta",
  "BodyPartExamined": "HEAD",
  "PatientPosition": "HFS",
  "ProcedureStepDescription": "MRI Brain",
  "SoftwareVersions": "27\\LX\\MR Software release:DV26.0_R03_1831.b",
  "MRAcquisitionType": "2D",
  "SeriesDescription": "EDTI_2mm_MB2_cdif45_AP",
  "ProtocolName": "[XT-ID:20-HG-0147]_NCR_3",
  "ScanningSequence": "EP\\RM",
  "SequenceVariant": "NONE",
  "ScanOptions": "CL_GEMS\\SAT_GEMS\\EDR_GEMS\\EPI_GEMS\\HYPERBAND_GEMS\\PFF\\FS",
  "PulseSequenceName": "edti",
  "ImageType": [
    "ORIGINAL",
    "PRIMARY",
    "OTHER"
  ],
  "SeriesNumber": 14,
  "AcquisitionTime": "14:50:55.000000",
  "AcquisitionNumber": 1,
  "SliceThickness": 2,
  "SpacingBetweenSlices": 2,
  "SAR": 0.410538,
  "EchoTime": 0.088,
  "RepetitionTime": 5.826,
  "FlipAngle": 90,
  "PhaseEncodingPolarityGE": "Flipped",
  "ShimSetting": [
    3,
    3,
    -17
  ],
  "PrescanReuseString": "RN/s7",
  "CoilString": "32Ch Head",
  "MultibandAccelerationFactor": 2,
  "PercentPhaseFOV": 100,
  "PercentSampling": 100,
  "AcquisitionMatrixPE": 110,
  "ReconMatrixPE": 128,
  "EffectiveEchoSpacing": 0.000601323,
  "TotalReadoutTime": 0.076368,
  "PixelBandwidth": 3906.25,
  "PhaseEncodingDirection": "j",
  "ImageOrientationPatientDICOM": [
    1,
    -0,
    0,
    -0,
    1,
    0
  ],
  "InPlanePhaseEncodingDirectionDICOM": "COL",
  "ConversionSoftware": "dcm2niix",
  "ConversionSoftwareVersion": "v1.0.20220720",
  "MultipartID": "dwi_1"
}

(I added MultipartID manually to see if it’d help the issue, but it didn’t).

The crash log is attached crash-20221223-182440-sudregp-concat-e65edb77-6e5c-4b05-9e24-ecb7ac025533.txt. And for completeness, here’s the initial qsiprep output:

This dataset appears to be BIDS compatible.
        Summary:                  Available Tasks:        Available Modalities: 
        18 Files, 197.13MB                                T1w                   
        1 - Subject                                       dwi                   
        1 - Session                                       bold                  


        If you have any questions, please post on https://neurostars.org/tags/bids.

221223-16:28:01,860 nipype.workflow INFO:         Running with omp_nthreads=8, nthreads=32
221223-16:28:01,860 nipype.workflow IMPORTANT:
         
    Running qsiprep version 0.16.1:
      * BIDS dataset path: /lscratch/54848062/31942/BIDS.
      * Participant list: ['test4'].
      * Run identifier: 20221223-162801_14cbc70e-5f4a-4537-80a6-cd3e18659b17.
    
221223-16:28:02,847 nipype.workflow INFO:         Combining all dwi files within each available session:
221223-16:28:02,847 nipype.workflow INFO:
                - 2 scans in session baseline
221223-16:28:02,861 nipype.workflow INFO:
         [{'dwi_series': ['/lscratch/54848062/31942/BIDS/sub-test4/ses-baseline/dwi/sub-test4_ses-baseline_dir-AP_run-1_dwi.nii.gz'], 'dwi_ser
ies_pedir': 'j', 'fieldmap_info': {'suffix': 'rpe_series', 'rpe_series': ['/lscratch/54848062/31942/BIDS/sub-test4/ses-baseline/dwi/sub-test4_
ses-baseline_dir-PA_run-1_dwi.nii.gz']}, 'concatenated_bids_name': 'sub-test4_ses-baseline_run-1'}]221223-16:28:02,924 nipype.workflow IMPORTANT:
         Creating dwi processing workflow "dwi_preproc_ses_baseline_run_1_wf" to produce output sub-test4_ses-baseline_run-1 (1.05 GB / 55 DWI
s). Memory resampled/largemem=1.21/1.26 GB.

Let me know if you need more details!

Thanks,

Gustavo