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Dear Min J,

You can get FA values using spm_summarise. A post by Guillaume will be useful.

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;e6c153de.1405

I wrote a tiny script to get the mean FA within mask(s) and save the
value in csv file.
This script simply uses spm_summarise to get the FA values within mask
(you can even select several masks) and calculate the mean value.
This might be what you are looking for.

Hope this helps,

Kiyotaka

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%%%%%mean_FA.m
% Get the mean FA values within mask(s)

%Select FA images
img = spm_select(inf,'image','Select FA images');

%Select mask images
msk = spm_select(inf,'image','Select mask images');

for j = 1:size(msk,1);
    roi = msk(j,:);

    for i = 1:size(img,1);
        data = spm_summarise(img(i,:),roi);
        output(i,j) = mean(data);
    end

end

%Save the result as a csv file
today = datestr(date);
filename = ['mean_FA_' today '.csv'];
csvwrite(filename,output);

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2014-06-09 1:50 GMT+09:00 KimMJ <[log in to unmask]>:
> Dear SPM experts
>
> I'm performing FA (fractional anisotropy) analysis between two groups
> (controls and patients) and want to extract individual values from the
> cluster of significant group difference for all subjects.
> For this purpose, I first saved the result of significant group difference
> (FWE-corrected P < 0.05) as a 'mask.img'.
> I then made a binary mask image ('mask_bin.img') using ImCalc function of
> 'i1>1'.
> My question is how I can obtain individual FA value from this mask for all
> subjects' FA data?
>
> Apology for the basic question.
> Thank you in advance for your help.
>
> Min J



-- 
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]