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SPM  September 2007

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Subject:

Re: Search Volume Size

From:

Ged Ridgway <[log in to unmask]>

Reply-To:

Ged Ridgway <[log in to unmask]>

Date:

Tue, 11 Sep 2007 14:43:01 +0100

Content-Type:

text/plain

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Hi Stephen,

> I also tried creating a new image, and summing the voxels within it, however
> that gave a different response to both the actual volume, and volume given
> by SVC. I'll use one of my ROI's in one of my paradigms as an example. The
> actual volume (given by both Marsbar and Analyze) is 1685mm^3; the volume
> given by SVC in SPM is 1236mm^3; and the volume I obtain using your method
> is 1488mm^3. 

That's odd... how exactly did you generate this last image and derive 
its volume? Use imcalc, select first the results directory mask.img, 
and then the ROI (sorry, I probably didn't say this carefully last 
time), and use the expression '(i1>0).*(i2>0)' then to get the volume 
of this in mm^3, you'd want something like:

   vol = spm_vol('new_mask.img');
   img = spm_read_vols(vol);
   Nvx = sum(img(:) > 0)
   vxv = abs(det(vol.mat));
   Nmm = Nvx * vxv

If I do this, with a 1mm isotropic ROI mask, and a 2mm isotropic 
analysis mask, then I exactly reproduce the mm^3 output shown in the 
SVC window.

> as I'm unsure whether using SVC, the whole ROI volume was searched for
> activation? Reading through your previous email on SVC, I'm assuming the
> whole volume ROI volume is searched through, and as such I should use the
> actual volume (i.e., 1685mm^3) when determining percentage of activated
> voxels within ROI...

First up, as I mentioned before, the SVC will not search voxels in the 
ROI if they are outside the original analysis mask. Its 1236 is 
therefore the volume it searched, and not your 1685, which ignores the 
analysis mask. (however, you should hopefully be able to reproduce 
1236 using the above method). Secondly, since this is a big 
discrepancy, I think you must be using something like absolute or 
relative threshold masking in your analysis, which you perhaps don't 
want if you really want to search all of your SVC ROI. So check that. 
And/or check whether your ROI goes outside the brain/GM, which you 
maybe don't want either.

If you want to compare results with your ROI on different methods 
and/or subjects, then possibly you might want to use your volume 
anyway, rather than the potentially different volumes for each set of 
results (since the analysis mask.img could be different, even without 
threshold masking, since constant voxels are masked out). Your results 
would then be a percentage of the *maximum* possible number of voxels 
searched, not the number that the SVC actually looked at. Does that 
sound a reasonable compromise?

Lastly, note that I still think my understanding of the code in the 
following thread is correct, which means that SVC will additionally be 
ignoring voxels that are below your initial whole-brain statistical 
threshold (though these voxels are counted for the search volume 
calculation), so you'll probably want to make sure you choose a lax 
uncorrected threshold for this, before proceeding with SVC.

http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=spm&P=7672

Sorry if any of this is unclear,

Ged

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