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MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
http://micapipe.readthedocs.io
GNU General Public License v3.0
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"RepetitionTime is missing in" #109

Closed hoptman closed 5 months ago

hoptman commented 5 months ago
hoptman commented 5 months ago

Hi all, I am enjoying the micapipe tool. I'm now trying to do the -proc_surf stage, but I now get the message "RepetitionTime is missing in", but when I look at the corresponding .json file, The RepetitionTime field is correctly populated.

I'm using micapipe v. 0.2.0 on Ubuntu Linux 20.04. The files are named like "_ses-BAS1_task-rest_acq-TR1400_bold.nii" Thanks, Matt

rcruces commented 5 months ago

can you please copy and paste the json file.

hoptman commented 5 months ago

Here you go:

{ "InPlanePhaseEncodingDirectionDICOM": "COL", "ImageComments": "Unaliased_MB4_PE3", "ProcedureStepDescription": "RESEARCH_colcombe", "DeviceSerialNumber": "35390", "AcquisitionMatrixPE": 112, "ImageOrientationPatientDICOM": [ 1, 0, 0, 0, 0.991216, -0.132256 ], "EffectiveEchoSpacing": 0.000689998, "TotalReadoutTime": 0.0765898, "ManufacturersModelName": "TrioTim", "ProtocolName": "REST_1400", "PhaseEncodingDirection": "j-", "BandwidthPerPixelPhaseEncode": 12.94, "RepetitionTime": 1.4, "SeriesNumber": 4, "PhaseEncodingSteps": 84, "MRAcquisitionType": "2D", "SliceThickness": 2, "AcquisitionNumber": 1, "InstitutionName": "Nathan_Kline_Institute_for_Psychiatric_Research", "DwellTime": 2.5e-06, "TxRefAmp": 312.696, "MultibandAccelerationFactor": 4, "DerivedVendorReportedEchoSpacing": 0.000689998, "SAR": 0.11055, "PulseSequenceDetails": "%CustomerSeq%_cmrr_mbep2d_bold", "ScanningSequence": "EP", "Manufacturer": "Siemens", "ConversionSoftware": "dcm2niix", "PercentPhaseFOV": 100, "ReconMatrixPE": 112, "FlipAngle": 65, "ConversionSoftwareVersion": "v1.0.20180403 GCC5.4.0", "SeriesDescription": "REST_1400", "PartialFourier": 0.75, "InstitutionAddress": "Old_Orangeburg_Road_140_Orangeburg_NY_US_10962", "ShimSetting": [ -2298, -361, 20600, 387, 523, 467, -658, -155 ], "AcquisitionTime": "13:35:3.482500", "SequenceName": "epfid2d1_112", "MagneticFieldStrength": 3, "TaskName": "rest", "SpacingBetweenSlices": 2, "ImageType": [ "ORIGINAL", "PRIMARY", "M", "ND", "MOSAIC" ], "ReceiveCoilName": "32Ch_Head", "EchoTime": 0.03, "SequenceVariant": "SK", "PhaseResolution": 1, "BaseResolution": 112, "PixelBandwidth": 1786, "ScanOptions": "PFP_FS", "SoftwareVersions": "syngo_MR_B17", "StationName": "MRC35390", "Modality": "MR", "InstitutionalDepartmentName": "Department", "PatientPosition": "HFS", "SliceTiming": [ 0, 0.615, 1.2275, 0.4375, 1.0525, 0.2625, 0.8775, 0.0875, 0.7025, 1.3175, 0.525, 1.14, 0.35, 0.965, 0.175, 0.79, 0, 0.615, 1.2275, 0.4375, 1.0525, 0.2625, 0.8775, 0.0875, 0.7025, 1.3175, 0.525, 1.14, 0.35, 0.965, 0.175, 0.79, 0, 0.615, 1.2275, 0.4375, 1.0525, 0.2625, 0.8775, 0.0875, 0.7025, 1.3175, 0.525, 1.14, 0.35, 0.965, 0.175, 0.79, 0, 0.615, 1.2275, 0.4375, 1.0525, 0.2625, 0.8775, 0.0875, 0.7025, 1.3175, 0.525, 1.14, 0.35, 0.965, 0.175, 0.79 ] }

hoptman commented 5 months ago

Hi again, I figured out that I had named the file incorrectly (I had specified it using -mainScanStr). Sorry to bother you! Best wishes, Matt