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help > RE: Warning: Assuming mosaics saved in reverse order due to 'sSliceArray.ucImageNumb'
Feb 19, 2023 04:02 AM | Chris Rorden
RE: Warning: Assuming mosaics saved in reverse order due to 'sSliceArray.ucImageNumb'
Hello,
Your images were acquired with H>>F image numbering mode. Siemens explicitly says you should not use this mode. Please adjust the sequence on your console. Some users assume that this acquires data in a descending rather than an ascending pattern, but this is not the case. It simply changes the order that 2D slices are written to the mosaic. I assume dcm2niix is doing the right thing, but this is virtually untested as Siemens explicitly warns users not to use this mode. Do check the spatial direction, the slice timing and the diffusion vectors if you use this mode. there is very little validation of this mode by dcm2niix (and presumably Siemens as well).
https://crnl.readthedocs.io/stc/index.ht...
see PDF by Joachim Graessner linked here https://en.wikibooks.org/wiki/SPM/Slice_...
"Do not use the mode H>>F because this complicates the numbering and you will have to sort images manually in most fMRI post-processing tools. The excitation of the slices in this case also starts caudally with the highest image numbers counting backwards!"
Your images were acquired with H>>F image numbering mode. Siemens explicitly says you should not use this mode. Please adjust the sequence on your console. Some users assume that this acquires data in a descending rather than an ascending pattern, but this is not the case. It simply changes the order that 2D slices are written to the mosaic. I assume dcm2niix is doing the right thing, but this is virtually untested as Siemens explicitly warns users not to use this mode. Do check the spatial direction, the slice timing and the diffusion vectors if you use this mode. there is very little validation of this mode by dcm2niix (and presumably Siemens as well).
https://crnl.readthedocs.io/stc/index.ht...
see PDF by Joachim Graessner linked here https://en.wikibooks.org/wiki/SPM/Slice_...
"Do not use the mode H>>F because this complicates the numbering and you will have to sort images manually in most fMRI post-processing tools. The excitation of the slices in this case also starts caudally with the highest image numbers counting backwards!"
Threaded View
| Title | Author | Date |
|---|---|---|
| neal_caffrey | Feb 19, 2023 | |
| Chris Rorden | Feb 19, 2023 | |
| larawa | Jul 6, 2023 | |
| Chris Rorden | Jul 6, 2023 | |
| larawa | Jul 13, 2023 | |
| Chris Rorden | Jul 13, 2023 | |
