Hi,
On 15 Jul 2009, at 19:46, Heather C. wrote:
> Hello,
>
> I am running contrast masks on each subject in my lower level
> analysis. For
> one such mask, I am masking contrast 7 with contrast 8, which shows
> up like
> this in my report log:
>
> /usr/local/fsl/bin/fslmaths thresh_zstat7 -mas stats/zstat8
> conmask/thresh_zstat7
>
> I have a few questions about this.....
>
> 1. Why is it masking a z stat image (stats/zstat8) onto a
> thresholded image
> (thresh_zstat7)?
Presumably because you asked it to? If you selected the "zstat>0"
option then this is what you're asking for. The "-mas" option uses
wherever the following argument is >0 as the mask.
>
> 2. What exactly are the thresholded images (e.g. thresh_zstat7) and
> how do
> they differ from a regular zstat image (e.g.zstat7)?
The latter is unthresholded and the former is thresholded according to
whatever thresholding you selected in the FEAT GUI.
>
> 3. It appears that the original thresh_zstat7 is being overwritten
> by the
> new contrast masked thresh_zstat7...is this correct?
Yes
>
> 4. Does this mean I want to look at thresh_zstat7 for my new contrast
> masked image and that zstat7 is my old, original contrast 7 image
> that is
> unaffected by the contrast mask?
Not quite -see above.
>
> 5. Is there an easy way to get the contrast masked images to be named
> something new, or some way to create them without overwriting any of
> the
> original contrast images?
The easiest thing to do would be to run FEAT twice, with and without
the contrast masking.
>
> Thank you so much for your help!
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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