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Siemens XA partial volumes in 4D datasets #742

@neurolabusc

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@neurolabusc

For 4D timeseries (T2* fMRI, DWI) Siemens XA enhanced format DICOM will generate one file for each 3D volume. However, if the series is interrupted, a valid DICOM is generated with fewer slices than other images in the series. For example, for a fMRI series with 48 slices, all complete volumes might report:

(0028,0008) IS [48]  #   2, 1 NumberOfFrames

However, if the series is interrupted, the final volume might only save six slices:

(0028,0008) IS [6]  #   2, 1 NumberOfFrames

Since NIfTI requires each volume in a 4D series have the same number of slices, dcm2niix will currently save the data as two files: one 4D image with 48 slices and one 3D image with 6 slices. However, this requires one of the images gets the a suffix appended to the filename to avoid name clashes. However, since the images are tied, one can not be certain if the complete or partial volumes will get the suffix. A better solution would be to discard partial volumes. There are two solutions:

  1. Complete volumes should have values 0..NumberOfFrames-1 in MultistepIndex (0021,115E). This is not the case for partial or interleaved partial volumes. However, this detection fails for partial volumes with sequential acquisition.
  2. The undocumented element ICE_Dims[20] of
    ICE_Dims (0021,118e) appears to store the number of slices for a complete acquisition (e.g. 48). This is a good solution if this is the consistent usage of this array element:
 (0021,118e) ST [X_1_1_1_1039_1_1_29_1_1_9_1_114_1_1_1_1_2000_2_1_48_1_1] #ICE_Dims

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