Dear Fred,
First, your question is related to modulation in VBM.
The following links explain how modulation works.
http://dbm.neuro.uni-jena.de/vbm/segmentation/modulation/
http://en.wikibooks.org/wiki/SPM/VBM#.22Modulation.22
The file you use for your pseudocode is modulated image, so you want
to calculate volume of the image.
Second, you can find various codes to calculate volume in SPM-ML.
For example, see the links below.
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;9c87d11f.0907
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;e8337a0.1207
Ged Ridgway provides a very useful script "get_totals.m", with which
you can compute volumes easily.
http://www0.cs.ucl.ac.uk/staff/G.Ridgway/vbm/get_totals.m
Hope this helps,
Kiyotaka
2014-10-26 5:45 GMT+09:00 Fred Sampedro <[log in to unmask]>:
> Any help on that? It would be something like computing the SUVmean in a ROI
> within a normalized PET scan? I've seen it in a number of papers but never
> explained how to compute it (gray matter volume or GMV).
>
> On Thu, Oct 23, 2014 at 6:37 PM, Fred Sampedro <[log in to unmask]>
> wrote:
>>
>> Dear SPM experts,
>>
>> Even after reading the related posts on this list I am wondering if I am
>> correctly computing an scalar grey matter volume in a particular ROI. First
>> of all, is there any difference between GM volume and GM density?
>>
>> Here is my pseudocode approach to compute the GM volume for each processed
>> scan (smwc1) in MNI space:
>>
>> gmfile = read ('smwc1XXX.nii');
>> roifile = read('roi.nii'); %binary roi in MNI space and with the same
>> dimensions that gmfile
>> prod = gmfile .* roifile;
>> GM_volume = sum(prod(:));
>>
>>
>> Is that correct?
>>
>> Thanks a lot!
>> Fred
>
--
Kiyotaka Nemoto, M.D., Ph.D.
Assistant Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: [log in to unmask]
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