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Re: Search Volume Size

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Wed, 12 Sep 2007 10:22:40 +1000

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 ```Hi Ged, OK... I've followed your steps, and get a different result again... this time I get 1531mm^3, so I'm not too sure what's going on?! Regarding the threshold masking... that option, to my understanding, is only available in 2nd level analysis, whereas I am using 1st level analysis to determine individual results, rather than group results for ROI (due to large variability in brains in my groups, as the majority are older adults aged > 70 years). I think I will use the whole volume, as it is a constant volume which can be used for analysis of the two functional tasks I have used for the study. Thanks for all your help... I'm still stuck on the volume SVC reports though?! Regards, Stephen. -----Original Message----- From: Ged Ridgway [mailto:[log in to unmask]] Sent: Tuesday, 11 September 2007 11:43 PM To: Stephen Duma Cc: [log in to unmask] Subject: Re: [SPM] Search Volume Size 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```