Hi Doug,

As the freesurferwiki says, the h.nii contains the estimated hemodynamic response at each voxel, along with the standard deviation of the residual error,
and h-offset.nii  contains a map of the mean value at each voxel.
My expectation is that h.nii should have the same dimension as my fmc.nii (the raw time course).
 For example, my fmc.nii is 90*90*60*256, where 256 is the TRs.  But the h.nii is only a 3D array 90*90*60. Why doesn't the h.nii have all the TRs?
I also have h0.nii and h0-offset.nii, what are these volume?

Thanks,

Yang


On Tue, Aug 9, 2011 at 1:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
You're using a fairly old version of freesurfer. If you have to use this, then use mkanalysis-sess (without the .new).
doug

Yang Liu wrote:
After I run recon-all -version, it shows: "v 1.133.2.57 2009/08/06'.
Since we have a lot of scripts for the older version, we kept using the old one.
If we don't use mkanalysis-sess.new, what we shall use?

Yang



On Tue, Aug 9, 2011 at 12:51 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   Yes, but don't use mkanalysis-sess.new. Are you not using version 5.X?
   doug

   Yang Liu wrote:

       Hi Doug,

       Thank you for prompt reply.
       So I should remove '-gammafit', and add '-fir 4 24' is for
       mkanalysis-sess.new?



       Yang

       On Tue, Aug 9, 2011 at 11:42 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:

          If you want a time course, you should use an FIR model,
       something
          like "-fir 4 24" to start the time window 4 sec before the
          stimulus onset and stop it 20 sec after stimulus onset. Do not
          include -gammafit.

          doug

          Yang Liu wrote:

              Hi all,

              I want to plot the hemodynamic response of a voxel after my
              analysis finishes. I hope I can get the hemodynamic
       response
              of each voxel for each session, so I can see the
       statistics by
              myself.

              My analysis.cfg is below:

              -gammafit 0 8
              -gammaexp 0.3
              -timewindow 40.0000
              -prestim 0
              -polyfit 2
              -TER 2.0000
              -autowhiten 40
              -nskip 0
              -fwhm 0
              -extreg mcextreg
              -nextreg 3
              -rescale 1000


              After I ran selxavg-sess, I got the following volumes:
       h0.nii,
              h0-offset.nii, h.nii, h-offset.nii, rstd.nii, rvar.nii.
              How can I get a response from these volumes?

              Yang


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