Do I have to specify the slice time when running 3dTshift?

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1

Hello AFNI experts,

I collected fMRI data with Multiband factor 2.
My question is: Do I have to specify the slice time when running 3dTshift?
Or, does afni program refer to the slice time information in .HEAD file??

I copied a part of my afni proc script.
================================= tshift =================================
foreach run ( $runs )
3dTshift -tzero 0 -quintic -prefix pb02.$subj.r$run.tshift
pb01.$subj.r$run.despike+orig
end

And I cheked the slice time of files before/after running 3dTshift.

$ 3dinfo -slice_timing pb01.pilot_r1.r01.despike+orig
0.000000|0.720000|0.028800|0.748800|0.057600|0.777600|0.086400|0.806400|0.115200|0.835200|0.144000|0.864000|0.172800|0.892800|0.201600|0.921600|0.230400|0.950400|0.259200|0.979200|0.288000|1.008000|0.316800|1.036800|0.345600|1.065600|0.374400|1.094400|0.403200|1.123200|0.432000|1.152000|0.460800|1.180800|0.489600|1.209600|0.518400|1.238400|0.547200|1.267200|0.576000|1.296000|0.604800|1.324800|0.633600|1.353600|0.662400|1.382400|0.691200|1.411200

$ 3dinfo -slice_timing pb02.pilot_r1.r01.tshift+orig
0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000

I think pb02 is the timing corrected one, but I’m asking this question because I could not find the post that directly answers my question.

2

By default 3dTshift will use the header information. You can override this with the -tpattern option. From the 3dTshift help:

  -tpattern ttt = use 'ttt' as the slice time pattern, rather
                  than the pattern in the input dataset header;
                  'ttt' can have any of the values that would
                  go in the 'tpattern' input to to3d...
3

As @pmolfese notes, you can pass it along. But it is better to have it correct in the EPI header to begin with, and yours does not look correct because it seems to be simply alt+z right now, and not like there is a multiband factor of 2 in it.

echo '0.000000 | 0.720000 | 0.028800 | 0.748800 | 0.057600 | 0.777600 | 0.086400 | 0.806400 | 0.115200 | 0.835200 | 0.144000 | 0.864000 | 0.172800 | 0.892800 | 0.201600 | 0.921600 | 0.230400 | 0.950400 | 0.259200 | 0.979200 | 0.288000 | 1.008000 | 0.316800 | 1.036800 | 0.345600 | 1.065600 | 0.374400 | 1.094400 | 0.403200 | 1.123200 | 0.432000 | 1.152000 | 0.460800 | 1.180800 | 0.489600 | 1.209600 | 0.518400 | 1.238400 | 0.547200 | 1.267200 | 0.576000 | 1.296000 | 0.604800 | 1.324800 | 0.633600 | 1.353600 | 0.662400 | 1.382400 | 0.691200 | 1.411200' | tr ' | ' ' ' > timing.txt
afni_python_wrapper.py -listfunc -print -float timing_to_slice_pattern `cat timing.txt`

How were the datasets constructed to have this timing?

- rick