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> 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
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--
Shahin Nasr

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