Well, that is bad (beacuse there is a bug) and good (because now it is known) at the same time.
I wanted to estimate a p-value for a group of voxels of interest for a certain contrast in my analysis. Instead of averaging the p values for these voxels, I thought it would make more sense to calculate the average t statistic for the voxels and then estimate the p-value for the group of voxels myself using tcdf function in matlab. So, I guess I need the t values for that, unless I can think of a workaround, which so far I couldn't. 

Best,
Pablo

On Thu, Nov 11, 2010 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
Hi Pablo, you have found a bug in FSFAST in which the values in the t.nii file are actually the sqrt of the p-values. I have fixed it in our code base and it will be in the next version. Do you actually need the t-values?

thanks!

doug

Pablo Polosecki wrote:
I understand the X.mat contains the variable DOF which tells me the degrees of freedom for the analysis, right? In my case it is 5915. This is what I get when I load X.mat into a structure named 'x':

x =

         DoSynth: 0
        UseFloat: 0
       SynthSeed: -1
           flac0: [1x1 struct]
         runflac: [1x21 struct]
               X: [6048x133 double]
             DOF: 5915
             rfm: [1x1 struct]
      yrun_randn: []
   RescaleFactor: 5.6510
       ErrCovMtx: 0
          acfseg: [1x1 struct]
        acfsegmn: [6048x1 double]
      nrho1segmn: 0.1456
               W: [6048x6048 double]



On Thu, Nov 11, 2010 at 11:35 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   what is your dof?

   Pablo Polosecki wrote:

       Oh, sure. It is:


       t.vol(test_voxel_number)

       ans =

         -0.6368


       On Thu, Nov 11, 2010 at 10:25 AM, Douglas N Greve
       <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
       <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

          sorry, I meant what is the actual value of the t in
          t.vol(test_voxel_number)?

          Pablo Polosecki wrote:

              Firstly, thank you for the quickyresponse.

              t.vol is the t-volume, loaded from t.nii using the MRIread
              function (i.e. t=MRIread('t.nii');). test_voxel_number
       is just
              some voxel of the volume that I'm using as an example
       in this
              sanity check  (I set it to 4000 in the sample code but it
              could have been anything else). I'm using
              -(abs(t.vol(test_voxel_number)
              )) because that is how I think the p-value is
       calculated from
              the t-statistic is a 2 tailed test.  (See for instance the
              matlab code of the built-in ttest.m function where you
       have p
              = 2 * tcdf(-abs(tval), df)  with df being the degrees of
              freedom.)  Still if I used the alternative you sugggest,
              without the minus sign, I get:

              my_pval=-log10(2*tcdf((abs(t.vol(test_voxel_number))),
       x.DOF))

              my_pval =

                -0.1690

              While I still have the stored p-value of

              stored_pval =

                -0.4055


              Thanks again!
                       On Thu, Nov 11, 2010 at 10:02 AM, Douglas N Greve
              <greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>
       <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>>
              <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>
              <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

                 what is t.vol(test_voxel_number)? Why do you use
                 -(abs(t.vol(test_voxel_number))) instead of
                 +(abs(t.vol(test_voxel_number)))?

                 doug

                 Pablo Polosecki wrote:

                     Dear experts,

                     For different reasons I found myself double
       checking the
                     relationship between t-values in t.nii and p-values
              stored in
                     sig.nii. If I use the following matlab code I
       thought
              that I
                     should get the values of my_pval and stored_pval
       to be the
                     same (except perhaps for the sign):

                     cd(fullfile(basedir,session,'bold',anal,contrast))
                     x=load('../X.mat')
                     t=MRIread('t.nii');
                     sig=MRIread('sig.nii');
                     test_voxel_number=4000;
                            my_pval=-log10(2*tcdf(-(abs(t.vol(test_voxel_number))),
              x.DOF))
                     stored_pval=sig.vol(test_voxel_number)



                     However I get:
                     stored_pval =

                       -0.4055

                     my_pval =

                        0.2804

                     Am I doing something wrong here? My FreeSurfer
       version
              is 4.5
                     Thank you!

                     --         Pablo Polosecki
                     Graduate Fellow
                     Laboratory of Neural Systems
                     The Rockefeller University
                     1230 York Avenue, Box 9
                     New York, NY 10065



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MGH-NMR Center
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