Stephanie Wrote:
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> Yes now it opened.

Good.

> However, I am assuming that I
> made the ROI with the wrong file now. I identified
> the ROIs with opening suma with this command:
>
> suma -spec 118_both.spec -sv 118_SurfVol+orig
>
> However, I made the ROI with
> ROIgrow -overwrite -spec std.141.118_lh.spec
> -surf_A std.141.lh.smoothwm.asc -roi_nodes
> nodevalue_all_ROIs_lh.1D -lim 6 -full_list
> -roi_labels nodelabel_all_ROIs_lh.1D -prefix
> ROImask_118_lh
>
> So now the ROI is in the wrong spot. Originally I
> did try to us the spec surface of 118_both.spec
> with ROIgrow, but was not able to get the ROIgrow
> command to work.

Can you provide more details? Did you get an error message?

> I am assuming I have to recreate
> the ROI 1D files with ROIgrow with a different
> surface input?

Probably. Most likely you probably need the same surface to use for ROIgrow as you use for visualizing the results, and also the indices for the nodes used to define the ROIs must match those.

I don't have enough information to give more guidance, as I don't know what surfaces are defined in 118_both.spec and how they were generated (for example, whether they are in correspondence with the standardized surfaces with ld=141). If you run suma with 118_both.spec and go to the nodes that you are using for the ROI, are they in the correct location?