Dear Afraim,
> Does anyone know how to run the slice timing
> correction in batch mode? Is it a hidden
> feature? Any Hacks?
Personally I use it via the function call, as there's not too much to enter
interactively. For example:
TR = 3;
slices = 20; % no of slices
gap = 0.05; % time after end of last slice acquisition, start of next volume
st = (TR-gap)/slices; % time to collect one slice
timeopt = 3; % which is the interleaved option for slice timing
refslice = 1 % slice for time 0
imgs = spm_get('files', 'mydirectory', 'myfiles*.img');
spm_slice_timing(imgs, timeopt,refslice,[st st+gap]);
You run into problems if you need a custom slice order, but you can easily add
that to the function if you need to; we have added our default of 1 3 5 .. 2 4
6..
Best,
Matthew
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