Re: [Freesurfer] problem with generating cesvar.nii

If you don't care about extending your results beyond your sample, then an FFx is fine. doug

SHAHIN NASR wrote:

Do you suggest using random-effect model? Is there any problem with using a fix-effect model (other than the fact that by using this model we can not predict response of subjects outside our population)?

On Wed, Oct 19, 2011 at 3:07 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

It should be roughly the sum of the dofs of the individual
subjects. Why are you using a fixed-effects model?
doug

SHAHIN NASR wrote:

      Thanks Doug. Just one related question. Should I also
    generate a new ffxdof.dat file for this map? I assumed that
    ffxdof depends on the number of subjects (session) and since
    number of subjects (sessions) is the same between the two
    groups then I can use those values, generated by
    isxconcat-sess for either map1 or map2. Right?



    On Wed, Oct 19, 2011 at 1:33 PM, 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:

       Hi Shahin, it is not as simple as doing a subtraction of the
       cesvar files. What you are trying to get is the expected
    variance
       of your difference between the ces files (as a variance, it
    must
       be positive). To get this you need

       cesvardiff = (cesvar1+cesvar2)/(2^2)

       The 2^2 is the number of inputs (2) squared.

       doug


       SHAHIN NASR wrote:

           Hi,

            I have generated two different functional connectivity
    maps
           for two different ROI-based seeds. These maps are based on
           group-average of the same subjects (generated by using
           separate isxconcat-sess commands ), and now I want to
    see the
           difference map. To do so, I used mris_calc as below.
           > mris_calc -o diff_map/rh.ces.nii   map1/rh.ces.nii  
    sub          map2/rh.ces.nii

           Also, to generate the rh.cesvar.nii file I used this
    command:
            > mris_calc -o diff_map1/rh.cesvar.nii  
     map1/rh.cesvar.nii
             sub   map2/rh.cesvar.nii

           But then when I used the glmfit with WLS option as below:

           > mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls
           --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii
           --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls
    rh.cesvar.nii

            I faced an error saying: "Error: MRInormWeights:
    values less
           than or eq to 0" which I assumed is related to an error in
           rh.cesvar.nii file (am I right?). Would you tell me how
    can I
           fix this problem?

           P.S.: please note that sequence of subjects and all MRI
           parameters are exactly the same between the two maps.

           --         Shahin Nasr

           PhD in Cognitive Neuroscience
           Martinos Imaging Center, MGH
           Harvard Medical School


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

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    -- 
    Shahin Nasr

    PhD in Cognitive Neuroscience
    Martinos Imaging Center, MGH
    Harvard Medical School


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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

-- Shahin Nasr

PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School