I want the time course for each voxel in my ROI.  But the time course should be corrected by removing the drift, which I think that is what the -polyfit option does.
I know I probably can do it myself, but I am wondering if Freesurfer has this already.

Yang 

On Wed, Aug 10, 2011 at 1:55 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
It is more accurate to say that it has the regression coefficients for the HRF. If you use a gamma or spm hrf, then it just has the amplitude (your case). If you use an FIR, then it has the coefficients for each delay in the FIR, which can be assembled into a waveform. I'm not sure what you are looking for if you want something that is equal to the number of time points. What do you want to do with it?
doug

Yang Liu wrote:
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 <mailto: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>
       <mailto: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>>
              <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:

                 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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