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Tom Ross
March 05, 2003 09:27AM
Christine Smith wrote:

> 3) Use 3dcalc to create a mask out of only those clusters
> present in the OFC. So assuming your OFC clusters are #3 and
> #5:
>
> 3dcalc -expr '(1-bool(a-3))*((1-bool(a-5))*2)' -a
> groupmap_clustorder_thresholded+tlrc -prefix OFC_clusters_mask

You probably wanted '(1-bool(a-3)) + ((1-bool(a-5))*2)', as there are not many voxels whose value is both 3 and 5. You could also use rect(a-3) instead of 1-bool(a-3) if you are lazier and want to type less.


> 4) For each contrast, use 3dROIStats to sample each subject's
> thresholded data with your mask.
>
>
> foreach subject (subj1 subj2 subj3)
>
> 3dROIstats -voxcount -mask OFC_clusters_mask+tlrc
> ${subject}.thresholded_contrast1+tlrc >>OFC_voxcount
>
> end

In the spirit of laziness, why not:
3dROIstats -voxcount -mask OFC_clusters_mask+tlrc *thresholded_contrast1+tlrc*HEAD >> OFC_voxcount


Tom

Subject Author Posted

How do I apply 3dclust to only "Activated" voxels within a mask?

Jim Bjork March 04, 2003 02:20PM

Re: How do I apply 3dclust to only "Activated" voxels within a mask?

Christine Smith March 04, 2003 07:18PM

Re: How do I apply 3dclust to only "Activated" voxels within a mask?

Tom Ross March 05, 2003 09:27AM

Re: How do I apply 3dclust to only "Activated" voxels within a mask?

Christine Smith March 05, 2003 07:33PM

Re: How do I apply 3dclust to only "Activated" voxels within a mask?

Jim Bjork March 06, 2003 09:55AM



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