Hi,
If you want to create a binary mask of overlap between two thresholded
zstat maps (etc) you can use something like
fslmaths thresh_zstat1 -mul thresh_zstat2 -bin overlap_mask
Then you can apply this to any other thresholded zstat map and rerun
"cluster" to get out the local maxima, e.g.
fslmaths thresh_zstat3 -mas overlap_mask masked_thresh_zstat3
cluster -i masked_thresh_zstat3 -t 0.0001 --olmax=grot
Cheers.
On 6 Feb 2009, at 16:33, Lisa Evans wrote:
> Hello,
>
> I wondered if anybody could help me with some masking issues. I
> have run a
> within-participants experiment with 4 tasks (1,2,3,4: each a
> separate scan),
> with three conditions in each task: 1A,1B,1C, 2A, 2B, 2C….
> Initially I ran a
> first-level analysis for each participant computing the contrasts
> that I was
> interested in (e.g. 1A+1B-1C etc). I then ran a higher-level mixed
> analysis
> computing the grand average of these contrasts. I am therefore able
> to see
> areas of activation within each task. What I’d like to do now is
> look at the
> areas of unique and common activation between pairs of tasks, in
> particular
> looking at the contrast A+B-C. What’s the best way of doing this?
>
> I have attempted the inclusive masking. I’ve generated binary masks
> of
> activations for A+B-C in task 1 and 2 and then used the fslmaths
> command –
> mul to look at common activation. Is this correct? Using this
> method I am able
> to see the areas of activation using fslview, however I wondered if
> there is
> any way of getting a list of the clusters and some z-coordinates?
>
> Finally, with regard to the exclusive masking I’m not sure of the
> best way to
> go about doing this, both theoretically and practically. So
> detailed advice on
> this would be much appreciated!
>
> Thanks very much.
>
---------------------------------------------------------------------------
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
---------------------------------------------------------------------------
|