Hi all,
I’m new to MRtrix and have run into a problem with dwifslpreproc. I’ve run all the conversion and denoising processes successfully, but when I try to run the dwifslpreproc, I get this error:
===========
eddy_openmp
===========
Reading images
EDDY::: EddyUtils::get_groups: Inconsistent b-values detected
EDDY::: EddyUtils.cpp::: static bool EDDY::EddyUtils::get_groups(const std::vector<EDDY::DiffPara>&, std::vector<std::vector<unsigned int> >&, std::vector<unsigned int>&, std::vector<double>&): Exception thrown
EDDY::: EddyUtils.cpp::: static bool EDDY::EddyUtils::GetGroups(const std::vector<EDDY::DiffPara>&, std::vector<std::vector<unsigned int> >&, std::vector<double>&): Exception thrown
EDDY::: ECScanClasses.cpp::: std::vector<std::vector<unsigned int> > EDDY::ECScanManager::GetShellIndicies(std::vector<double>&) const: Exception thrown
EDDY::: Eddy failed with message EDDY::: ECScanClasses.cpp::: EDDY::ECScanManager::ECScanManager(const string&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, EDDY::ECModel, EDDY::ECModel, const std::vector<unsigned int>&, const EDDY::PolationPara&, EDDY::MultiBandGroups, bool): Exception thrown
I’ve searched around for the “inconsistent b-values error” and found a couple of people with the same issue, but none of them seemed resolved. One thing to note is that I used the -json_import and -fslgrad options in the mrconvert. They seemed to write OK and no errors, but I wanted to make sure that wasn’t part of the problem. When I run mrinfo on the denoised_unr.mif file this is what I get:
Image name: “sub-b097_ses-01_dir-AP_dwi_den_gibbs.mif”
Dimensions: 128 x 128 x 60 x 81
Voxel size: 2 x 2 x 2.5 x 2.4
Data strides: [ -1 2 3 4 ]
Format: MRtrix
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 0.9837 0.07 0.1655 -138.4
-0.05271 0.9929 -0.1066 -132.6
-0.1718 0.09619 0.9804 -62.97
AcquisitionDuration: 216.222
AcquisitionMatrixPE: 128
AcquisitionNumber: 1
AcquisitionTime: 13:09:12.265000
BandwidthPerPixelPhaseEncode: 22.6450005
BaseResolution: 128
BodyPartExamined: BRAIN
CoilCombinationMethod: Adaptive Combine
CoilString: HeadNeck_64_CS
ConversionSoftware: dcm2niix
ConversionSoftwareVersion: v1.0.20220720
Dcm2bidsVersion: 2.1.7
DerivedVendorReportedEchoSpacing: 0.000689997978
DeviceSerialNumber: 175689
DiffusionScheme: Monopolar
DwellTime: 2.30000001e-06
EchoTime: 0.0869999975
EchoTrainLength: 47
EffectiveEchoSpacing: 0.000344998989
FlipAngle: 90
ImageOrientationPatientDICOM: 0.983729,-0.0527124,0.17175,0.0699969,0.992899,-0.096186
ImageType: ORIGINAL
PRIMARY
DIFFUSION
NONE
ImageTypeText: ORIGINAL
PRIMARY
DIFFUSION
NONE
ND
ImagingFrequency: 123.223999
InPlanePhaseEncodingDirectionDICOM: COL
InstitutionAddress: Trinity 1601B,Austin,Houston,US,78712
InstitutionName: UT Health Austin 3T
InstitutionalDepartmentName: Radiology
MRAcquisitionType: 2D
MTState: false
MagneticFieldStrength: 3
Manufacturer: Siemens
ManufacturersModelName: MAGNETOM Vida
Modality: MR
MultibandAccelerationFactor: 4
NonlinearGradientCorrection: false
ParallelAcquisitionTechnique: SMS
ParallelReductionFactorInPlane: 2
PartialFourier: 0.75
PartialFourierDirection: PHASE
PatientPosition: HFS
PercentPhaseFOV: 100
PercentSampling: 100
PhaseEncodingDirection: j-
PhaseResolution: 1
PixelBandwidth: 1698
ProtocolName: dwi_acq-80direc_dir-AP
PulseSequenceDetails: %SiemensSeq%\ep2d_diff
PulseSequenceName: *epse2d1_128
ReceiveCoilActiveElements: HC1-7;NC1
ReceiveCoilName: HeadNeck_64_CS
ReconMatrixPE: 128
RefLinesPE: 30
RepetitionTime: 2.4000001
ScanOptions: PFP\FS
ScanningSequence: EP
SequenceVariant: SK\SP
SeriesDescription: dwi_acq-80direc_dir-AP
SeriesNumber: 17
ShimSetting: -1766,-1902,9400,589,-215,217,283,-11
SliceThickness: 2.5
SliceTiming: 0,1.27,0.16,1.4275,0.3175,1.5875,0.4775,1.745,0.635,1.905,0.795,2.0625,0.9525,2.2225,1.1125,0,1.27,0.16,1.4275,0.3175,1.5875,0.4775,1.745,0.635,1.905,0.795,2.0625,0.9525,2.2225,1.1125,0,1.27,0.16,1.4275,0.3175,1.5875,0.4775,1.745,0.635,1.905,0.795,2.0625,0.9525,2.2225,1.1125,0,1.27,0.16,1.4275,0.3175,1.5875,0.4775,1.745,0.635,1.905,0.795,2.0625,0.9525,2.2225,1.1125
SoftwareVersions: syngo MR XA31
SpacingBetweenSlices: 2.5
StationName: AWP175689
TotalReadoutTime: 0.0438
TxRefAmp: 318.677002
command_history: /opt/mrtrix3/bin/mrconvert /scratch/06865/waw758/dwi_pipeline_testing/BIDS/sub-b097/ses-01/dwi/sub-b097_ses-01_dir-AP_dwi.nii.gz /scratch/06865/waw758/dwi_pipeline_testing/derivatives/fmriprep-v23.1.3/sub-b097/ses-01/dwi/sub-b097_ses-01_dir-AP_dwi.mif -json_import /scratch/06865/waw758/dwi_pipeline_testing/BIDS/sub-b097/ses-01/dwi/sub-b097_ses-01_dir-AP_dwi.json -fslgrad /scratch/06865/waw758/dwi_pipeline_testing/BIDS/sub-b097/ses-01/dwi/sub-b097_ses-01_dir-AP_dwi.bvec /scratch/06865/waw758/dwi_pipeline_testing/BIDS/sub-b097/ses-01/dwi/sub-b097_ses-01_dir-AP_dwi.bval (version=3.0.4)
/opt/mrtrix3/bin/dwidenoise /scratch/06865/waw758/dwi_pipeline_testing/derivatives/fmriprep-v23.1.3/sub-b097/ses-01/dwi/sub-b097_ses-01_dir-AP_dwi.mif /scratch/06865/waw758/dwi_pipeline_testing/derivatives/fmriprep-v23.1.3/sub-b097/ses-01/dwi/sub-b097_ses-01_dir-AP_dwi_den.mif -noise /scratch/06865/waw758/dwi_pipeline_testing/derivatives/fmriprep-v23.1.3/sub-b097/ses-01/dwi/noise.mif (version=3.0.4)
/opt/mrtrix3/bin/mrdegibbs /scratch/06865/waw758/dwi_pipeline_testing/derivatives/fmriprep-v23.1.3/sub-b097/ses-01/dwi/sub-b097_ses-01_dir-AP_dwi_den.mif /scratch/06865/waw758/dwi_pipeline_testing/derivatives/fmriprep-v23.1.3/sub-b097/ses-01/dwi/sub-b097_ses-01_dir-AP_dwi_den_gibbs.mif -axes ‘0,1’ (version=3.0.4)
comments: TE=87;Time=130912.265;mb=4
dw_scheme: 0,0,0,0
[81 entries] 0,0,0,0
…
0.4388540849,-0.8646261074,-0.2445992368,1200
0,0,0,0
mrtrix_version: 3.0.4
Has anyone resolved this issue or know what’s going on? Let me know if you need any more info on my data.
Thanks!
Wade