slice_timing

AFNI Message Board
1

Hello AFNI experts!!

I am having an issue with my fMRI data. I found that when I do 3dinfo -slice_timing in my EPI images the timing is “0”. We found a solution to “called back” the slice timing information 3dTcat topup_corrected_Rest.nii -tpattern alt+z -prefix EPI_fixed.nii which seems to work. But when I want to use this “fixed” data, and do, for example 3dTshift, the slice timing is again reset to “0”.

Do you have any suggestions on how to address this?

2

3dinfo -slice_timing EPI_retroicor.nii
0.000000|1.000000|0.055556|1.055556|0.111111|1.111111|0.166667|1.166667|0.222222|1.222223|0.277778|1.277778|0.333333|1.333334|0.388889|1.388889|0.444444|1.444445|0.500000|1.500000|0.555556|1.555556|0.611111|1.611112|0.666667|1.666667|0.722222|1.722223|0.777778|1.777778|0.833333|1.833334|0.888889|1.888890|0.944445|1.944445

3dinfo -slice_timing EPI_tshift.nii
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|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

3

Do you mean the slice timing of the output of 3dTshift is all zero? If so, that is intended, since the timing has been altered by the program, interpolating each time series to adjust the apparent acquisition time.

  • rick
4

Thank you for all Rick!!!