my experiment uses an EPI scan with a TR of 2s. 36 slices in total. The .json output from dcm2niix looks like this:
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?
Does nobody know an answer?
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