Confusion about Slicing timing correction

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?

Best wishes,

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?

  • rick

Dear rick,

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?

Best wishes,

Hi Peng,

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.

  • rick

Dear rick,

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.

Dear rick,

Great thanks for help me solving this long-standing confusing problem!!!

Hope all barriers been removed in your way!

Best wishes,