What is the reference slice in my 3dTshift code?

AFNI Message Board
1

Hi AFNI experts,
My fMRI data were acquired with 26 slices in descending sequence. I used the code below for timing correction before:


3dTshift -tpattern seq-z -quintic -prefix pb01.sub1.r01.tshift pb00.sub1.r01.tcat+orig

Now I need report the timing correction parameters in my manuscript. But I am not sure what is the reference slice used in my code.I have checked the usage of 3dTshift and found two options are designed for setting the reference slice. But one of them has no default reference and I don’t know which option is used in the default state.
So I need help from you.
Thank you!
Yu

2

Hi,

You could specify a slice as the reference using the -tzero or -slice options. But the default is to use the average.


The default alignment time is the average
of the 'tpattern' values (either from the
dataset header or from the -tpattern option)
3

Thank you, Peter!
The average is the default to the ‘-tpattern’ option. But the default of ‘-slice’ option is not provided in the help link. We don’t know which option is activated preferentially if the reference slice is not inputted. If the ‘-slice’ option is activated in this situation, I need to know its default reference.

4

If you don’t specify either, the program uses the default mentioned above. If you add the -verbose flag to the command it will output what the “common time point” is set to. In afni_proc.py, the default is to use a -tzero 0 (align to the first).

5

Thank you!
So the average of the ‘tpattern’ values is the default reference time.
But I am not sure what is the exact meaning of “the average of the ‘tpattern’ values”.
The timing correction code is :


3dTshift -tpattern seq-z -quintic -prefix pb01.sub1.r01.tshift pb00.sub1.r01.tcat+orig

And the TR is 2 s in my experiment.
So I guess the average of the ‘tpattern’ values is 1 s?
I don’t know whether I have guessed right.
But this seems to be not so reasonable.
Take the example in the usages of 3dtshift for example:


                 slice number
tpattern    0   1   2   3   4    
   --------- --- --- --- --- ---   - 
   altplus     0 600 200 800 400   
   alt+z2    400   0 600 200 800    
   altminus  400 800 200 600   0    
   alt-z2    800 200 600   0 400    
   seqplus     0 200 400 600 800   
   seqminus  800 600 400 200   0


All  the averages of the tpatterns listed above are 400 ms. That doesn't make sense because all the default references are same though the tpatterns are different.

Your reply will be highly appreciated!

6

The average tpattern time works fine; it tends to be
approximately in the middle of the TR (slightly less
than that). You are right, the average tpattern does
not depend on the acquisition. I do not see why it
should. Bob made the default at the midpoint so
that the average time shift is minimized.

Note that afni_proc.py uses a default of the beginning
the TR, since that generally makes the timing align
with the stimulus timing.

  • rick