On Feb 20, 2013, at 3:02 PM, Sudhin A. Shah wrote:

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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Hi Sudhin

are you sure that the NaNs don't exist before registration and extraction? Cany you check? I don't see why anything we would have done would introduce them.

cheers Bruce On Fri, 22 Feb 2013, Sudhin A. Shah wrote:

        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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  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  greve@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422

  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

  _______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


  The information in this e-mail is intended only for the person to whom it is
  addressed. If you believe this e-mail was sent to you in error and the e-mail
  contains patient information, please contact the Partners Compliance HelpLine at
  http://www.partners.org/complianceline . If the e-mail was sent to you in error
  but does not contain patient information, please contact the sender and properly
  dispose of the e-mail.

---

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.