Hi Heiner,
sorry, yes these are two different scans. I should have selected MRI2, not MRI1 (as MRI2 is the one I mentioned is having issues with voxel placement).
Here is the output (MRI2)
Filename: '/data/project/SV2A_MC1/LEV/sourcedata/sub-223/ses-MRI2/20-ACC_svs_se_30_noECC/resources/secondary/2.25.32491572345396840739318711101525313657-20-1-anwtlt.dcm'
FileModDate: '05-Aug-2024 09:41:00'
FileSize: 116584
Format: 'DICOM'
FormatVersion: 3
Width: 1
Height: 1
BitDepth: []
ColorType: ''
FileMetaInformationGroupLength: 174
FileMetaInformationVersion: [2×1 uint8]
MediaStorageSOPClassUID: '1.2.840.10008.5.1.4.1.1.4.2'
MediaStorageSOPInstanceUID: '2.25.256577899615104464943943200131520304722'
TransferSyntaxUID: '1.2.840.10008.1.2.1'
ImplementationClassUID: '1.2.40.0.13.1.1'
ImplementationVersionName: 'dcm4che-2.0'
SpecificCharacterSet: 'ISO_IR 100'
ImageType: 'ORIGINAL\PRIMARY\SPECTROSCOPY\NONE'
SOPClassUID: '1.2.840.10008.5.1.4.1.1.4.2'
SOPInstanceUID: '2.25.256577899615104464943943200131520304722'
StudyDate: '20240703'
SeriesDate: '20240703'
ContentDate: '20240703'
AcquisitionDateTime: '20240703133314.540000'
StudyTime: '131848.400000'
SeriesTime: '133803.344000'
ContentTime: '133803.348000'
AccessionNumber: '2.25.290070988920337595058960832122557831312'
Modality: 'MR'
Manufacturer: 'Siemens Healthineers'
StudyDescription: '223 Placebo Synaptic_Connectivity'
SeriesDescription: 'ACC_svs_se_30_noECC'
PerformingPhysicianName: [1×1 struct]
ManufacturerModelName: 'MAGNETOM Prisma'
ReferencedImageEvidenceSequence: [1×1 struct]
VolumetricProperties: 'DISTORTED'
VolumeBasedCalculationTechnique: 'NONE'
ComplexImageComponent: 'COMPLEX'
AcquisitionContrast: ''
Private_0009_10xx_Creator: 'SIEMENS SYNGO INDEX SERVICE'
Private_0009_108c: ''
PatientName: [1×1 struct]
PatientID: '223_Placebo'
PatientSex: 'M'
PatientAge: '056Y'
PatientSize: 1.7780
PatientWeight: 77
DeidentificationMethod: 'RSU XNAT Migration Anonymisation'
DeidentificationMethodCodeSequence: [1×1 struct]
BodyPartExamined: 'HEAD'
MagneticFieldStrength: 3
DeviceSerialNumber: '166001'
SoftwareVersions: 'syngo MR XA30'
ProtocolName: 'ACC_svs_se_30'
SpatialResolution: 1
DateOfLastCalibration: '20090304'
TimeOfLastCalibration: '123723'
B1rms: 0.4742
PatientPosition: 'HFS'
ContentQualification: 'PRODUCT'
PulseSequenceName: '*svs_se'
EchoPulseSequence: 'SPIN'
MultipleSpinEcho: 'NO'
MultiPlanarExcitation: 'NO'
SteadyStatePulseSequence: 'NONE'
EchoPlanarPulseSequence: 'NO'
SpectrallySelectedSuppression: 'NONE'
GeometryOfKSpaceTraversal: 'RECTILINEAR'
SegmentedKSpaceTraversal: 'SINGLE'
RectilinearPhaseEncodeReordering: 'LINEAR'
SpectralWidth: 2500
ChemicalShiftReference: 4.7000
VolumeLocalizationTechnique: 'PRESS'
Decoupling: 'NO'
KSpaceFiltering: 'NONE'
TimeDomainFiltering: 'NONE'
NumberOfZeroFills: 0
BaselineCorrection: 'NONE'
AcquisitionDuration: 288
NumberOfKSpaceTrajectories: 96
TransmitterFrequency: 123.2563
ResonantNucleus: '1H'
FrequencyCorrection: 'NO'
VolumeLocalizationSequence: [1×1 struct]
ApplicableSafetyStandardAgency: 'IEC'
FirstOrderPhaseCorrection: 'NO'
WaterReferencedPhaseCorrection: 'NO'
MRSpectroscopyAcquisitionType: 'SINGLE_VOXEL'
StudyInstanceUID: '2.25.32491572345396840739318711101525313657'
SeriesInstanceUID: '2.25.281001225998221136498368569177969505290'
SeriesNumber: 20
AcquisitionNumber: 1
InstanceNumber: 1
FrameOfReferenceUID: '2.25.183037375415414858825769564518733185486'
PositionReferenceIndicator: ''
DimensionOrganizationSequence: [1×1 struct]
DimensionIndexSequence: [1×1 struct]
Private_0021_10xx_Creator: 'SIEMENS MR MRS 05'
Private_0021_11xx_Creator: 'SIEMENS MR SDR 01'
Private_0021_1001: 300.5098
Private_0021_1101: 'ACQUISITION'
Private_0021_1102: 'ACQUISITION'
NumberOfFrames: 1
Rows: 1
Columns: 1
DataPointRows: 1
DataPointColumns: 2048
SignalDomainColumns: 'TIME'
DataRepresentation: 'COMPLEX'
PerformedProcedureStepStartDate: '20240703'
PerformedProcedureStepStartTime: '131848.400000'
PerformedProcedureStepEndDate: '20240703'
PerformedProcedureStepID: 'USa47e067974314b'
PerformedProcedureStepDescription: '223 Placebo Synaptic_Connectivity'
AcquisitionContextSequence: [1×1 struct]
IssueDateOfImagingServiceRequest: '20240703'
SharedFunctionalGroupsSequence: [1×1 struct]
PerFrameFunctionalGroupsSequence: [1×1 struct]
SpectroscopyData: [4096×1 single]
I have managed to run it with nifti files recently but with some workarounds.
- I select no PDF output in the job file (per errors mentioned here)
- I have to specify the basis file, because unlike with dicoms it can no longer identify the right one automatically.
- When it gets to coregistration and segmentation I get an error about unknown vendor so I just type
MRSCont.vendor = 'Siemens';in the terminal and then I continue running the script with:MRSCont = OspreyCoreg(MRSCont); MRSCont = OspreySeg(MRSCont);
It’s not the most optimal but using nifti files does place the voxels in correct locations, so at least it works.