mahshid Wrote:
-------------------------------------------------------
> Hi all,
>
> Thanks very much for your helps.
>
> Ziad,
> I tried using SurfExtrema as what you said,
> SurfExtrema -i
> subj_surface/SUMA/std.141.lh.smoothwm.asc -input
> tt.1D.dset -hood 15 -thresh 0 -gthresh 0 -prefix
> isodist
>
> But the file isodist.ext.1D.dset did not contain
> only 1s, but 1 to 476, so in next step ROIgrow
> made 476 seprate files

It is a lot of files from ROIgrow but they can be combined to give you what you want. But before we proceed on this, does looking at any of these files look like the ROI you want from one of these locations? You mention that the regions are not quite circular, but I don't expect them to be. Nodes are considered within Xmm from each other if the shortest path between them along the mesh (walking along connected edges) is less than Xmm. You can display the surfaces in mesh mode (press 'p' once) to help understand what is going on.

cheers,
Ziad

but easily I loaded
> isodist.ext.1D.dset in Matlab and change all
> values (except 0s) to 1. so the modified
> isodist.ext itself is what I need, index of
> uniformly spaced ROIs with single vertices, and
> when I upload it in suma it looks good. But if I
> wanted to make circular ROIs including more than 1
> vertex, the ROIgrow seems not to work well. I
> used:
>
> ROIgrow -i
> subj_surface/SUMA/std.141.lh.smoothwm.asc
> -roi_labels isodist.ext.1D.dset -roi_nodes
> isodist.ext.1D.dset -lim 15 -full_list -prefix
> isodis.grow -overwrite
>
> I tried the case for both isodist.ext modified in
> MATLAB, and also tried to use all 476 files
> (overlapping them, or using them separately). but
> the output is not like uniformly spaced circles,
> so seems I am missing a point.
>
> Thanks again,
> Mahshid