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questions > RE: dcm2niix, slice timing and slice order
Jul 4, 2019 10:07 AM | Chris Rorden
RE: dcm2niix, slice timing and slice order
The slice times reported in the BIDS json file correspond to the
order that dcm2niix stores the slices to disk. This web page describes how dcm2niix infers slice timing and other details
from GE files. In general, dcm2niix converts images based on the
order or their instance number, and the vendor-specific DICOM tag
reveals the acquisition time for that slice. Unfortunately, the
DICOM standard does not require that instance number refers to
acquisition order (or is even unique). Therefore, if instance
number does not correspond with spatial position, dcm2niix orders
the slices based on spatial position and again uses the
corresponding time tag to infer the slice time of that slice. In
brief, NIfTI requires slices are saved in spatially sequential
order, so dcm2niix ensures this.
Also, I have heard reports but have not confirmed that some recent GE software releases use the single-band reference times for multi-band acquisition. Be aware that dcm2niix assume that the values in the DICOM header are truthful. This reflects an error in GE's DICOMs, not dcm2niix.
Also, I have heard reports but have not confirmed that some recent GE software releases use the single-band reference times for multi-band acquisition. Be aware that dcm2niix assume that the values in the DICOM header are truthful. This reflects an error in GE's DICOMs, not dcm2niix.
Threaded View
Title | Author | Date |
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Richard Parker | Jun 18, 2019 | |
Chris Rorden | Jun 18, 2019 | |
Richard Parker | Jul 3, 2019 | |
Chris Rorden | Jul 4, 2019 | |