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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Richard Parker Jun 18, 2019
RE: dcm2niix, slice timing and slice order
Chris Rorden Jun 18, 2019
Richard Parker Jul 3, 2019
Chris Rorden Jul 4, 2019