Hi Tyler,
We made this change a few years ago, see the log message below:
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r4915 | ged | 2012-09-11 18:38:30 +0100 (Tue, 11 Sep 2012) | 3 lines
Changed default reference time bin to 8 (t/2), which should be optimal
for the middle slice in non-interleaved acquisitions, not too far from
the middle slices in interleaved acquisitions, and close to optimal for
3D EPI. Changed help text a little too.
Changed spm_dcm_specify to set default VOI timings to be consistent with
the above, i.e. defaulting to RT/2 instead of RT.
------------------------------------------------------------------------
You can find another example of the effect of the choice of the
reference slice (ie microtime bin) in slide 41 of this presentation from
Rik Henson:
http://www.fil.ion.ucl.ac.uk/spm/course/slides02/ppt/event.ppt
This choice is a compromise and the 'new' default value is somehow the
'best' guess. Change it to reflect the reference slice from the slice
timing correction if you used it, or to be most sensitive to a specific
part of the brain depending on your acquisition scheme.
Best regards,
Guillaume.
On 22/02/18 19:16, Tyler Hein wrote:
> Hello again,
>
> Sorry for the second email! As I mentioned in my last email, I can
> replicate SPM8 FIR activation maps in SPM12 by changing the microtime
> settings in SPM12. Please see attached for two powerpoint figures - 1 of
> activation in SPM12 with SPM8 microtime settings, and 1 of activation in
> SPM12 with SPM12 microtime settings. I'm trying to decide which setting
> I should have students use; is one of these more correct than the other?
> Why did the microtime settings change from SPM8 to SPM12? I'd appreciate
> any recommendations you may have.
>
> Thank you again!
>
> Best,
> Tyler
>
> On Thu, Feb 22, 2018 at 11:31 AM, Tyler Hein <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Wiktor and Guillaume,
>
> Thank you so much for your guidance!
>
> Both analyses relied on the default value for microtime onset - when
> I set the microtime onset in SPM12 to 1 (the SPM8 default), I am
> able to replicate our results from before. Thank you again!
>
> Best,
> Tyler
>
> On Wed, Feb 21, 2018 at 5:56 AM, Guillaume Flandin
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Dear Tyler,
>
> It's quite difficult to provide you with an answer without knowing
> exactly how you run the two analyses in the two SPM versions but
> the one
> thing I can think of is the change of the default for the microtime
> onset t0 from 1 in SPM8 to 8 in SPM12. Are both analyses relying
> on SPM
> default value or is it encoded in the script/batch you are using?
>
> Best regards,
> Guillaume.
>
>
> On 19/02/18 02:07, Tyler Hein wrote:
> > For spm_orth.m, there is a new option in spm12 to include
> normalisation
> > in serial orthogonalisation, and the code that is executed for
> this
> > condition is identical to what was executed in spm8 under the
> default
> > condition. In spm12, the default condition now has different
> code. In
> > the instructions we give students, it does not indicate
> changing the
> > normalisation parameter from the default. However, I think
> this script
> > is executed for both canonical and FIR basis functions, so I'm
> not sure
> > that this would be the source of the differences in findings,
> either.
>
> --
> Guillaume Flandin, PhD
> Wellcome Trust Centre for Neuroimaging
> University College London
> 12 Queen Square
> London WC1N 3BG
>
>
>
>
> --
> Tyler C. Hein, M.S.
> Doctoral Candidate, Developmental Psychology
> University of Michigan, Ann Arbor
> [log in to unmask] <mailto:[log in to unmask]>
>
>
>
>
> --
> Tyler C. Hein, M.S.
> Doctoral Candidate, Developmental Psychology
> University of Michigan, Ann Arbor
> [log in to unmask] <mailto:[log in to unmask]>
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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