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.eduwrote:
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.**edugreve@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<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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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