Dear afni experts,
I’m doing slice timing correction for data from GE MR750 machine.
Up to now, i get the interleaved scan order from engineer, and find some interesting tags from DICOM header:
First scan Direction: Superior
First scan Location:75.135
Last scan Direction: Inferior
Last scan Location: -91.658
And I’ve checked that these two slice are the highest and lowest slice for 1 TR.
For the tpattern option from 3dTshift:
S L I C E N U M B E R
tpattern 0 1 2 3 4 Comment
--------- --- --- --- --- --- -------------------------------
altplus 0 600 200 800 400 Alternating in the +z direction
alt+z2 400 0 600 200 800 Alternating, but starting at #1
altminus 400 800 200 600 0 Alternating in the -z direction
alt-z2 800 200 600 0 400 Alternating, starting at #nz-2
seqplus 0 200 400 600 800 Sequential in the +z direction
seqminus 800 600 400 200 0 Sequential in the -z direction
I think i should choose between alt+z and alt-z, but I am quite confused with which one to choose with the information above, what’s the relationship between +z/-z and the information above? I can’t figure out where’s the corresponding Slice Number in my DICOM header, would you mind giving me some advice?
The +/-z there refer to with respect to the direction z is changing, not whether it goes from I to S or S to I. If the first slice acquired was the most superior and the last the most (or second most, depending on the parity) inferior, AND if the orientation shows S to I (e.g. RAS) in 3dinfo, say, then the timing pattern should be alt+z.
Note that this is a relative comparison between the temporal order of slices and the order of slices on disk. If they are the same it will be ‘+’, if not, a ‘-’.
What does 3dinfo -orient say about this dataset?
Here are the Information from 3dinfo：
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
which seems to be I to S on the disk, I think it should be alt-z according to your post above, am i right?
Yes, that does seem to be correct. But make sure that dataset has not been modified or anything. Have any commands been run on it already? If not, alt-z seems correct.
It’s the first step to run dcm2niix from MRIcron to convert dicom files to a single NIFTI file, nothing has done except this, is it okay?
Sure, that seems good. Thanks.
Great thanks for help me solving this long-standing confusing problem!!!
Hope all barriers been removed in your way!