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questions > RE: dcm2niix, slice timing and slice order
Jun 18, 2019 01:06 PM | Chris Rorden
RE: dcm2niix, slice timing and slice order
The slice timing values are with respect to the order that the 2D
slices are saved to disk. In you case, the first slice on disk was
acquired first, and the next slice as saved to disk was
acquired 0.1375 seconds later. This is how tools like FSL's
slicetimer and SPM expect the data to be reported. These slice
timing tools do not need to know anything regarding world-space
(x,y,z dimensions), they only work within image space (i,j,k). So
since you mention H>F, it suggests that your data was acquired
as axial slices. Therefore, if the first slice on disk is the
closest to the feet, with subsequent slices moving superior than
your acquisition was ascending in the head to foot direction. On
the other hand, if the first slice is the most superior, this is a
descending sequence. You can look at the header's QForm or SForm to
transform i,j,k (columns, rows, slices) to x,y,z (left-right,
posterior-anterior, inferior-superior). Alternatively, open the
preferences window in MRIcron and turn of image reorient/rotation
and load your data without spatial transforms.
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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 | |