Subject: | | Re: extremely large % signal change in ASL data |
From: | | Roberto Viviani <[log in to unmask]> |
Reply-To: | | [log in to unmask][log in to unmask]> wrote: > Dear Ged, > > thank you very much. It was easy... > By the way, as far as I understand, the colorbar displayed is the one with > the T values, right? Is it possibe to show a colorbar with p-values instead? > > Thanks. > > Regards, > > Joćo > > On Thu, May 6, 2010 at 11:42 AM, DRC SPM <[log in to unmask]> wrote: >> >> Dear Joćo, >> >> When you've got the glass brain results up in SPM, click the "save" >> button near the bottom right of the interactive window, and enter a >> filename for the output image. You should then be able to load this >> thresholded t-map as an overlay in MRIcroN etc. >> >> Note that you can display the blobs overlaid on an image in SPM itself >> too, just click the "overlays..." menu, and pick "sections" and then >> select an image you want to overlay onto (e.g. an average image, >> created by warping your original images with the same transformations >> used to create your VBM data, and then using imcalc with expression >> mean(X) and the data matrix (dmtx) flag true). If you've used DARTEL, >> the simplest thing to overlay onto is the GM of the final template, >> e.g. Template_6.nii. >> >> Hope that helps, >> Ged >> >> 2010/5/6 Joćo Duarte <[log in to unmask]>: >> > Dear SPMers, >> > >> > how can I display the map of significant blobs that is output of VBM >> > analysis in SPM8, using for example MRIcroN? >> > >> > Thanks in advance. >> > >> > Regards, >> > >> > Joćo >> > > >[log in to unmask] |
Date: | | Sun, 23 May 2010 08:19:21 +0200 |
Content-Type: | | text/plain |
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Dear Marieke,
> When extracting percent signal change of ASL perfusion data, I am
> getting extremely large and variable values, both positive and
> negative. In fact, values like -311 or 4653 are not uncommon.
> Obviously something is going very wrong here, but I don't know what.
The estimated CBF values are ratios of random variables, which gives
them a rather intractable distribution -- even if the original
variables were normal. The values you observe are not necessarily a
sign that your data are useless. Furthermore, at the pial surface and
at the base of the brain (most markedly in the cerebellum) the
variance is very high.
>
> I'm using a simple visual paradigm, with each trial consisting of a
> visual stimulus of about 2 seconds, followed by a fixation dot of
> about 20 seconds as baseline. I am using the ASL subtraction
> function of the ASLtbx, and I extract percent signal changes with
> MarsBar. In my model I include time and dispersion derivatives.
You'll probably have an effective TR of about 8 secs, so it will be
hard to pick up a signal of 2 secs (but you say below you saw
something). Given that the signal is quantitative, I see no advantage
in evaluating the effect with estimates of %signal change.
>
> The subtracted ASL images look fine, up to the point that they are
> fed into the SPM model. The localisation of significant voxels also
> looks right. However, the task related beta values range from, say,
> -70 to 70, and the baseline betas show about the same range of
> values. As a comparison, BOLD data of the same task shows task
> related beta values of about -2 to 2, and baseline beta values
> between, say 100 and 200.
The beta values are scaled to the regressor. So it is hard to say.
Also, it depends on whether these are average effect estimates; you
might well have peaks here or there.
> This observation does explain the high percent signal changes in the
> ASL data (for the BOLD data they are fine), but I don't understand
> why those beta values end up like this.
Well I guess it's a difference in philosophy, but to get an idea of
whether your signal has plausibility you'd have to compute the effect
of the task relative to baseline in ml/100g/min. The % signal change
contains less information than these two measurements. The baseline
beta values of BOLD have no meaning.
Best,
Roberto Viviani
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