Just a question on how to set up slice timing. P

reviously I used this code to set up the slice timing, but I'm not sure it is still correct, as it had been mentioned that it might be changed. That said, I'm wondering if I should use the following:

Option A (code that I used before):
opt.slice_timing.timing(1)=(TR-0.02)/nb_slices;
opt.slice_timing.timing(2) = opt.slice_timing.timing(1) + 0.02;

Option B (code that was used by someone else in my lab):
opt.bricks.slice_timing.timing(1)=TR/nb_slices; % time beetween slices
opt.bricks.slice_timing.timing(2)=TR/nb_slices; % time between the last slice of a volume and the first slice of next volume

Thanks for your help!

Hi Deb,

Slice timing is without any doubt a real pain. So option A is for a delay in TR of 0.02, while option B has no delay in TR. This way of specifying the timing corresponds to the "old" pre-0.6.4 NIAK. With the NIAK 0.6.4 you would simply not specify opt.slice_timing.timing. Instead you would write :

opt.slice_timing.delay_in_tr = 0.02;

for option A, and

opt.slice_timing.delay_in_tr = 0;

for option B. The old way was inspired by SPM and is still supported, but I wouldn't recommend going there. Same comments apply to the slice order. Please have a look at the tutorial :
http://www.nitrc.org/plugins/mwiki/index...

If you don't know if you had a delay in TR in your acquisition, have a look at the following post :
http://www.nitrc.org/forum/forum.php?thr...

Good luck with your analysis,

Pierre

Hi Pierre,

I have a delay in TR, so I will use:
opt.slice_timing.delay_in_tr = 0.02;

Thanks so much for your help! I really appreciate it. :)