README.md

About

dcm_qa_stc is a simple DICOM to NIfTI validator script and dataset to test slice timing correction. There is no standard way to report slice times in the DICOM format, so different vendors have developed different methods. Note that Philips does not encode slice times in their DICOM data.

GE

For details see GE page.

• GE/ProtocolDataBlock

  • source: https://github.com/neurolabusc/dcm_qa_nih
  • slice timing: Private Protocol Data Block (0025,101B) SLICEORDER tag
  • units: inferred from SLICEORDER (0=sequential, 1=interleaved), number of slices and TR. Note GE does not report delays between volumes so this estimate will be inaccurate for sparse designs (where slice timing correction is inadvisable).
  • note: four series provided: sequential and interleaved with inferior to superior and superior to inferior slice orders.
  • version: (0018,1020) LO [27_LX_MR_Software_release:DV26.0_R01_1725.a]

• GE/TriggerTime

  • source: https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Slice_timing_correction
  • slice timing: Trigger Time (0018,1060) "DS [187]"
  • units: milliseconds
  • version: (0018,1020) LO [24\LX\MR Software release:DV24.0_R02_1607.b]

• GE/RTIA

  • source: https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Slice_timing_correction
  • slice timing: RTIA Timer (0021,105E) "DS [4.314800]"
  • units: seconds
  • version: (0018,1020) LO [24\LX\MR Software release:DV24.0_R02_1607.b]

• GE/RTIAold

  • source: https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Archival_MRI
  • slice timing: RTIA Timer (0021,105E) "DS [23457.000000]"
  • units: 1/10,000 second
  • note: rordenlab/dcm2niix#286
  • version: (0018,1020) LO [14\LX\MR Software release:14.0_M4_0629.a]

Siemens

For details see Siemens page.

• Siemens/B12

  • source: https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Archival_MRI
  • slice timing: CSA Header does not include "MosaicRefAcqTimes", slice times can be inferred from "sSliceArray.ucMode".
  • units: NONE (inferred from TR and delayTimeInTR)
  • version: (0018,1020) LO [syngo MR 2006T 4VB12T]

• Siemens/B13

  • source: https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Archival_MRI
  • slice timing: CSA Header does not include "MosaicRefAcqTimes", slice times can be inferred from "sSliceArray.ucMode".
  • units: NONE (inferred from TR and delayTimeInTR)
  • version: (0018,1020) LO [syngo MR B13 4VB13A]

• Siemens/B15

  • source: https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Archival_MRI
  • slice timing: CSA Header (0029,1009) "MosaicRefAcqTimes"
  • units: msec
  • version: (0018,1020) LO [syngo MR B15]

• Siemens/B17

  • source: https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Archival_MRI
  • slice timing: CSA Header (0029,1009) "MosaicRefAcqTimes"
  • units: msec
  • version: (0018,1020) LO [syngo MR B17]

• Siemens/D13

  • source: https://www.mccauslandcenter.sc.edu/crnl/tools/stc
  • slice timing: CSA Header (0029,1009) "MosaicRefAcqTimes"
  • units: msec
  • note: Series 2 uses default Foot->Head mosaic, Series 10 stores Head->Foot mosaic. See source page for details.
  • version: (0018,1020) LO [syngo MR D13D]

• Siemens/E11

  • source: Development scan from McCausland Center
  • slice timing: CSA Header (0029,1009) "MosaicRefAcqTimes"
  • units: msec
  • version: (0018,1020) LO [syngo MR E11]

• Siemens/E11_2D

  • source: https://www.ndcn.ox.ac.uk/divisions/fmrib
  • slice timing: Series 3 (saved as mosaics) CSA Header (0029,1009) "MosaicRefAcqTimes", Series 8 (saved as 2D slices) Acquisition Time (0008,0032) "TM [105723.300000]"
  • units: msec, HHMMSS
  • note: acquisition time must handle slice times across midnight
  • version: (0018,1020) LO [syngo MR E11]

• Siemens/XA10

  • source: rordenlab/dcm2niix#240
  • slice timing: Time After Start (0021,1104) "DS [12.58]"
  • units: seconds
  • note: XA11 multi-band sequences can inaccurately report single-band values in 0021,1104
  • slice timing: Frame Acquisition Time (0018,9074) "DT [20181022083642.635000]"
  • units: YYYYMMDDHHMMSS
  • note: Siemens de-identification can scramble frame acquisition time
  • version: (0018,1020) LO [syngo MR XA10]

UIH

For details see UIH page.

• UIH/R002
  • source: rordenlab/dcm2niix#225
  • slice timing: AcquisitionTime (0008,0032) "TM [134052.312000]"
  • units: HHMMSS
  • note: must handle slice times across midnight
  • version: (0018,1020) LO [R002]