Confusion about Slicing timing correction

AFNI Message Board
1

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,
Peng

2

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
3

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,
Peng

4

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
5

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?

Best,
Peng

6

Sure, that seems good. Thanks.

7

Dear rick,

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

Hope all barriers been removed in your way!

Best wishes,
Peng