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Siemens slice timing. #322

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neurolabusc opened this issue Aug 7, 2019 · 0 comments
Closed

Siemens slice timing. #322

neurolabusc opened this issue Aug 7, 2019 · 0 comments

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@neurolabusc
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The pre-release dcm2niix v1.0.20190720 introduced a new method to determine slice timing from old Siemens datasets: using the "ucMode". An unintended consequence is that this algorithm would produce incorrect values for modern multi-band datasets where the tags MosaicRefAcqTimes and PATModeText (0021,1009) were missing. This is the unusual case where users of B17-E11 do not use the efficient Mosaic storage for multi-band (which dramatically increases the number of files).

The latest commit introduces an additional method to determine slice times, all documented here, with sample datasets here.

  1. Old systems (before B15): ucMode (note these systems pre-date multi band)
  2. 2D slices (B15-E11): Acquisition Time (0008,0032)
  3. 3D Mosaics (B15-E11): MosaicRefAcqTimes
  4. 4D series (XA10-11): Frame Acquisition Time (0018,9074)
neurolabusc added a commit that referenced this issue Aug 7, 2019
@neurolabusc
Document new Siemens slice timing (#322)
acb654d
neurolabusc added a commit that referenced this issue Aug 7, 2019
@neurolabusc
Siemens slice timing (#322)
270361e
neurolabusc added a commit to neurolabusc/dcm_qa_stc that referenced this issue Aug 7, 2019
@neurolabusc
Siemens slice timing (rordenlab/dcm2niix#322)
93af74a
@neurolabusc neurolabusc mentioned this issue Aug 23, 2019
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yarikoptic added a commit to neurodebian/dcm2niix that referenced this issue May 6, 2020
@yarikoptic
Merge commit '1.0.20190720+git34-g605ba61' into debian
2cb74e5 
* commit '1.0.20190720+git34-g605ba61':
  Document Philips non-image DICOMs (rordenlab#328)
  Handle Philips proprietary transfer syntax (https://discourse.slicer.org/t/fail-to-load-pet-ct-gemini/8158/6)
  Support big-endian (rordenlab#327)
  Emulate seriesUidCrc if SeriesUid does not exist
  change to -n (now uses CRC of SeriesUID) and version reporting (rordenlab#326)
  Siemens slice timing (rordenlab#322)
  Document new Siemens slice timing (rordenlab#322)
  Use Acquisition Time (0008,0032) to infer slice times for Siemens data saved as 2D slices not mosaic (MosaicRefAcqTimes missing).
  E11C 2D (not mosaic) files do not report mosaicAcqTimes or multi-band factor.
  Slice timing element order and scale fixes
  Adding missing preprocessor fence
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@neurolabusc