Hi there -
I'm guessing here, but I think it's possible you're
thresholding the wrong image. The threshold you type in is applied to
whichever image you have selected in the bottom left hand corner of
fslview. My guess is that you have selected the underlying structural
image and not the functional overlay. If you swap the selection, and then
apply the threshold to the overlay, it should threshold ok.
Tim
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Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
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On Mon, 23 Aug 2004, Jacquie H wrote:
> Hello -
> I'm new to fsl, and need a little help with a data-viewing inconsistency.
> I ran an analysis, and by looking at the FEAT report, could see that activations in my contrasts did
> not survive the clustered threshold analysis. When I view the data in AFNI, and threshold the
> image at 1.522, there are some nice (small) clusters of activation that I would like to use for an
> ROI analysis.
> Here's the problem: when I load the same .hdr file (it's a tstat image) into fsl view and try to
> threshold the image, there are enormous blobs of activation everywhere - the whole brain is
> almost red (even with ridiculously high thresholds).
> I'm wondering if anyone has encountered this problem before and could give me a little advice on
> getting the fslview images to more closely resemble the AFNI ones...
>
> Thanks!
> Jacquie
>
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