[MINC-users] functional connectivity problem with alternating slice pattern (Keith's way)

[Penhune Lab]

Thank you Andrew, I have an analysis running right now but will check this
and get back to you when it completes (sometime this evening or tomorrow).
Having looked at the images created by both ascending and descending
slicetimes for this analysis, my sense is that there is not that the
slicetimes don't make that much of a difference - and that this difference
is reflected in lower magnitude t-values rather than spurious results. Do
you think this is accurate?

Cheers,
Chris

On Mon, Jul 27, 2009 at 8:27 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Chris,
>
> On Tue, Jul 28, 2009 at 03:47, Penhune Lab<penhunelab at gmail.com> wrote:
> > problem: the mag_t.mnc files resulting from the analysis appear to have
> an
> > alternating slice pattern.
> >
> > I have already conducted simple model-based fmrilm analyses on this data
> set
> > and do not see this same alternating slice pattern in them. I acquired at
> a
> > resolution of 4mm^3 (interleaved ascending*) *on the BIC 3T. From what I
> can
> > tell, the issue arises because of the interleaved ascending slicetimes.
> If I
> > change the slicetimes from interleaved ascending to ascending the
> > alternating pattern disappears.
>
> Sounds to me like you are being bitten by slice scaling issues. MINC
> will scale each slice separately (and maintain an internal list of
> scaling values) to ensure the best range is stored for each slice as
> it is converted/processed. You seem to be using fmristat? which means
> you are using EMMA and I not sure as to how well EMMA handled slice
> scaling. My first approach to this problem would be to convert your
> input volume to float. When volumes are in float/double format slice
> scaling is not used.
>
>   mincreshape -float input.mnc input_float.mnc
>
> And then re-run the analysis.
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
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>



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