There's a slightly convoluted way to do this:
1. Run mri_surfcluster with --thmin y. Save the output cluster number
overlay with --ocn. This is a surface overlay where the value is the
cluster number.
2. Since the clusters are ordered based on descending peak vertex
value, you can create a mask from the ocn that only includes the
clusters where the peak is greater than your threshold. Eg, if
clusters 1-5 meet your critera the,
mri_binarize --max 5.5 --i ocn.mgh --o mask.mgh
3. Now apply the mask to your input sig:
mri_mask sig.mgh mask.mgh sig.masked.mgh
doug
On Tue, 19 Feb 2008, Catherine Hartley wrote:
Sorry for the delayed follow-up.
Doug, I don't think mri_surfcluster allows me to implement the criteria I
want (only include clusters containing a peak vertex above threshold x, but
vertices within those clusters can be included if they exceed threshold y
(where y < x).
Bruce, I am happy to do this manually but I'm not sure how. If I draw a
closed path around each cluster to be removed, how do I remove it and save
the sig.mgh file without the cluster. Likewise, If I click inside the
cluster and use custom fill to select it, how do I remove it from the sig.mgh
file, or at least make it invisible?
Thanks,
Cate
On Feb 11, 2008, at 7:19 PM, Bruce Fischl wrote:
Hi Cate,
is doing it manually an option? You could draw closed curves around each
cluster, or click in each one and use the custom fill in tksurfer. Is that
what you mean?
Bruce
On Mon, 11 Feb 2008, Catherine Hartley wrote:
Hi,
I'm wondering whether it is possible to create an overlay consisting of a
subset of clusters from a sig.mgh file, filtered according to custom
criteria and preserving the significance value of each vertex in the
remaining clusters so that the overlay can be thresholded as I choose.
For example, if I wanted to remove a selected set of ten clusters from a
sig.mgh file to yield a new one, is there an easy way to do this?
Thanks,
Cate
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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