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PS: In particular, if you use a within-TR delay, i.e. a delay period between consecutive volumes, it may be worth checking if the NIFTI entries on the slice timing are correct. Cheers, Andreas ________________________________________ Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Connolly, Colm [[log in to unmask]] Gesendet: Mittwoch, 13. April 2011 21:28 An: [log in to unmask] Betreff: Re: [FSL] AW: slice times and field map correction Hi, On Apr 12, 2011, at 9:37 PM, Andreas Bartsch wrote: > > not sure what you mean by 'slice times stored in the EPI file'. These are not stored in NIFTI. This is not quite correct. Having read the header file for the NIFTI1 file format it is clear that information about the slice times can be stored in the NIFTI1 header. For example, consider a acquisition as follows: TR=2s, 40 slices acquired (axially) in alternating +z direction which is stored in a file named rg.nii fslhd rg.nii tells us (among other things which I omit for the sake of brevity) pixdim[4] 2.0000000000 phase_dim 0 freq_dim 0 slice_dim 3 slice_name alternating_increasing slice_code 3 slice_start 0 slice_end 39 slice_duration 0.050000 freq_dim = phase_dim = 0 slice_dim = 3 tells us this was a spiral acquisition, that the slices were acquired in alternating increasing +z direction, that the start slice is 0 the end slice is 39 and that each slice is 0.05s apart. > Also: when you unwarp the geometric distortions of the functionals, you usually do so after motion correction. Here, the problem is that motion changes the slices timing, i.e. the two interact, but not the unwarping. > Does that makes sense? Yes, but still doesn't answer my question. If we assume that the nifti files contain the slice time info and we do not do motion correct before fieldmap unwarping, what happens to the slice time info present in the original files as they are propagated through the unwarping process? Regards, -- Colm G. Connolly, Ph. D. Dept of Psychiatry University of California, San Diego 9500 Gilman Dr. #0738 La Jolla, CA 92093-0738 Tel: +1-858-246-0684