Hello

I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat & aseg2feat)

When I extract the values (as per the matlab code below), I see NaNs in certain regions. Of the 19 datasets that I have analyzed I have see NaNs for the following labels

1006        1033        2006        2013    2033

Is this a known problem? Is there a solution?

Thanks,

S

On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:

Sorry, I don't think we have such a program. You could do it in matlab
fairly easily, eg,

f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
  ind = find(a.vol == seglist(nthseg));
  roimean(:,nthseg) = mean(fmat(:,ind),2);
end

m = roimean'*roimean;

On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:

Hello,

This worked perfectly 2 years ago :), but now I am having some trouble.

I run reg-feat2anat & aseg2feat with no problem.

I now need a correlation matrix of every ROI (created by freesurfer)

against every other ROI. For this I used @ROI_Corr_Mat

(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).

Again - this worked fine in the past.

Now I get an error (working with AFNI to see if it can be fixed).

Question: Is there any alternative to getting this correlation matrix?

i.e every ROI against every other ROI?

Thanks,

S

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