Quick question about slice timing and slice time correction

slicetiming
fmriprep

#1

Hello,

my experiment uses an EPI scan with a TR of 2s. 36 slices in total. The .json output from dcm2niix looks like this:
“SliceTiming”: [
0.99,
0,
1.045,
0.055,
1.1,
0.11,
1.155,
0.165,
1.21,
0.22,
1.265,
0.275,
1.32,
0.33,
1.375,
0.385,
1.43,
0.44,
1.485,
0.495,
1.54,
0.55,
1.595,
0.605,
1.65,
0.66,
1.705,
0.715,
1.76,
0.77,
1.815,
0.825,
1.87,
0.88,
1.925,
0.935 ]

So in the manual of fmriprep it states “All slices are realigned in time to the middle of each TR.”. Am I right to assume that this would mean they are realigned to the first slice in my case since it is acquired at (almost) 1s?

Thanks!


#2

Does nobody know an answer?


#3

FMRIPREP is using https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTshift.html to perform slice time correction without setting the -tzero argument which means the default behavior is triggered:

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

In your case that would be 0.9625s or roughly ~1s. Please mind that slice time correction is not performing spatial interpolation, but a temporal one. In other words, we are not interpolating to a particular slice, but to a particular time point. Here are a couple of great resources explaining the process: http://www.brainvoyager.com/bvqx/doc/UsersGuide/Preprocessing/SliceScanTimeCorrection.html http://andysbrainblog.blogspot.com/2012/09/slice-timing-correction.html