Open araikes opened 10 months ago
thanks a lot Adam for reporting this in detail - this seems like a clear bug on our part, and I will test it myself and get back to you shortly.
This is easier to share data if needed.
I think the log is very clear that the folder was skipped because it was identified as a phantom.
2023-10-20 08:12:29,049 - INFO - ACR/Phantom: /xdisk/adamraikes/app_apoe/dicoms/20230512_114500_apoemouse_APPCA_C1_VM6979_1_11/5/pdata/1/dicom
We tested on human datasets, and we rely on certain dicom tags to identify them as phantoms. If those tags were not populated, it may misidentify DICOM as a phantom
More complete tag list (though not all):
Dataset.file_meta -------------------------------
(0002, 0000) File Meta Information Group Length UL: 196
(0002, 0001) File Meta Information Version OB: b'\x00\x01'
(0002, 0002) Media Storage SOP Class UID UI: Enhanced MR Image Storage
(0002, 0003) Media Storage SOP Instance UID UI: 2.16.756.5.5.200.8323328.195705.1683918037.311.3.0
(0002, 0010) Transfer Syntax UID UI: Explicit VR Little Endian
(0002, 0012) Implementation Class UID UI: 1.2.276.0.7230010.3.0.3.6.6
(0002, 0013) Implementation Version Name SH: 'OFFIS_DCMTK_366'
-------------------------------------------------
(0008, 0005) Specific Character Set CS: 'ISO_IR 192'
(0008, 0008) Image Type CS: ['ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE']
(0008, 0012) Instance Creation Date DA: '20230512'
(0008, 0013) Instance Creation Time TM: '152313'
(0008, 0014) Instance Creator UID UI: 2.16.756.5.5.1020.360.13.23.30
(0008, 0016) SOP Class UID UI: Enhanced MR Image Storage
(0008, 0018) SOP Instance UID UI: 2.16.756.5.5.200.8323328.195705.1683918037.311.3.0
(0008, 0020) Study Date DA: '20230512'
(0008, 0021) Series Date DA: '20230512'
(0008, 0023) Content Date DA: '20230512'
(0008, 002a) Acquisition DateTime DT: '20230512121318.002-0700'
(0008, 0030) Study Time TM: '114500'
(0008, 0031) Series Time TM: '152313'
(0008, 0033) Content Time TM: '152313'
(0008, 0050) Accession Number SH: ''
(0008, 0060) Modality CS: 'MR'
(0008, 0070) Manufacturer LO: 'Bruker BioSpin MRI GmbH'
(0008, 0080) Institution Name LO: 'University of Arizona - Tucson'
(0008, 0090) Referring Physician's Name PN: 'bhattrai'
(0008, 0201) Timezone Offset From UTC SH: '-0700'
(0008, 103e) Series Description LO: '4_CIBS_MultishellDWI'
(0008, 1090) Manufacturer's Model Name LO: 'BioSpec 70/20'
(0008, 9121) Referenced Raw Data Sequence 1 item(s) ----
(0008, 1115) Referenced Series Sequence 1 item(s) ----
(0008, 1199) Referenced SOP Sequence 1 item(s) ----
(0008, 1150) Referenced SOP Class UID UI: Raw Data Storage
(0008, 1155) Referenced SOP Instance UID UI: 2.16.756.5.5.200.8323328.195705.1683917100.7.5
---------
(0020, 000e) Series Instance UID UI: 2.16.756.5.5.200.8323328.195705.1683918037.311
---------
(0020, 000d) Study Instance UID UI: 2.16.756.5.5.200.8323328.195705.1683917100.7
---------
(0008, 9205) Pixel Presentation CS: 'MONOCHROME'
(0008, 9206) Volumetric Properties CS: 'VOLUME'
(0008, 9207) Volume Based Calculation Technique CS: 'NONE'
(0008, 9208) Complex Image Component CS: 'MAGNITUDE'
(0008, 9209) Acquisition Contrast CS: 'DIFFUSION'
(0010, 0010) Patient's Name PN: 'apoemouse^^^^'
(0010, 0020) Patient ID LO: 'apoemouse'
(0010, 0030) Patient's Birth Date DA: '20230403'
(0010, 0040) Patient's Sex CS: 'O'
(0010, 1030) Patient's Weight DS: '0.001'
(0010, 2201) Patient Species Description LO: 'RODENT'
(0010, 2210) Anatomical Orientation Type CS: 'QUADRUPED'
(0010, 2292) Patient Breed Description LO: ''
(0010, 2293) Patient Breed Code Sequence 0 item(s) ----
(0010, 2294) Breed Registration Sequence 0 item(s) ----
(0010, 2297) Responsible Person PN: ''
(0010, 2299) Responsible Organization LO: 'University of Arizona - Tucson'
(0018, 0023) MR Acquisition Type CS: '3D'
(0018, 0087) Magnetic Field Strength DS: '7.05403738128'
(0018, 1000) Device Serial Number LO: '406491'
(0018, 1020) Software Versions LO: ['Acquisition PV-360.3.3', 'ParaVision 360.3.3']
(0018, 1030) Protocol Name LO: '4_CIBS_MultishellDWI'
(0018, 5100) Patient Position CS: 'HFP'
(0018, 9004) Content Qualification CS: 'PRODUCT'
(0018, 9005) Pulse Sequence Name SH: 'Bruker:DtiEpi'
(0018, 9008) Echo Pulse Sequence CS: 'BOTH'
(0018, 9011) Multiple Spin Echo CS: 'NO'
(0018, 9012) Multi-planar Excitation CS: 'NO'
(0018, 9014) Phase Contrast CS: 'NO'
(0018, 9017) Steady State Pulse Sequence CS: 'LONGITUDINAL'
(0018, 9018) Echo Planar Pulse Sequence CS: 'YES'
(0018, 9024) Saturation Recovery CS: 'NO'
(0018, 9025) Spectrally Selected Suppression CS: 'FAT'
(0018, 9029) Oversampling Phase CS: '3D'
(0018, 9032) Geometry of k-Space Traversal CS: 'RECTILINEAR'
(0018, 9034) Rectilinear Phase Encode Reordering CS: 'LINEAR'
(0018, 9064) k-space Filtering CS: 'NONE'
(0018, 9073) Acquisition Duration FD: 11392.0
(0018, 9093) Number of k-Space Trajectories US: 1
(0018, 9094) Coverage of k-Space CS: 'FULL'
(0018, 9100) Resonant Nucleus CS: '1H'
(0018, 9174) Applicable Safety Standard Agency CS: 'IEC'
(0020, 000d) Study Instance UID UI: 2.16.756.5.5.200.8323328.195705.1683917100.7
(0020, 000e) Series Instance UID UI: 2.16.756.5.5.200.8323328.195705.1683918037.311
(0020, 0010) Study ID SH: 'APPCA_C1_VM6979'
(0020, 0011) Series Number IS: '50001'
(0020, 0013) Instance Number IS: '1'
(0020, 0052) Frame of Reference UID UI: 2.16.756.5.5.200.8323328.195705.1683917100.7
(0020, 1040) Position Reference Indicator LO: ''
Hi @sinhaharsh , I think it is a bug on our part if we are doing "If those tags were not populated, it may misidentify DICOM as a phantom"
we should not filter out any image unless we are definitively sure its to be filtered (clear/direct evidence that it is phantom etc)
Description
Attempted to run this on mouse DICOMs from a Bruker 70/20 7-Tesla system running Paravision 360 v3.3 (backend software). Outputs include enhanced DICOMs. It appears to look for DICOMs in the right location but then reports no DICOMs
What I Did
Here's the contents of that folder:
Just as a sanity check: