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 <[email protected]>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 < >> [email protected] >> <mailto:[email protected].**edu<[email protected]>>> >> 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 >> <[email protected] >> <mailto:[email protected].**edu<[email protected]> >> > >> <mailto:[email protected].**edu <[email protected]> >> <mailto:[email protected].**edu <[email protected]>>>> >> 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 >> <[email protected] >> <mailto:[email protected].**edu <[email protected]>> >> <mailto:[email protected].**edu <[email protected]> >> <mailto:[email protected].**edu <[email protected]>>> >> <mailto:[email protected].**edu<[email protected]> >> <mailto:[email protected].**edu <[email protected]>> >> <mailto:[email protected].**edu<[email protected]> >> <mailto:[email protected].**edu <[email protected]>>>>> >> 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 >> >> >> ------------------------------** >> ------------------------------**------------ >> >> ______________________________**_________________ >> Freesurfer mailing list >> [email protected] >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> > >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> > >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >>> >> >> https://mail.nmr.mgh.harvard.** >> edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> <mailto:[email protected].**edu <[email protected]>> >> <mailto:[email protected].**edu<[email protected]> >> <mailto:[email protected].**edu <[email protected]>>> >> <mailto:[email protected].**edu<[email protected]> >> <mailto:[email protected].**edu <[email protected]>> >> <mailto:[email protected].**edu<[email protected]> >> <mailto:[email protected].**edu <[email protected]>>>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 >> <tel:617-724-2358>>> Fax: 617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> <tel:617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>>> >> >> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://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> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> >> >> The information in this e-mail is intended only for the >> person to >> whom it is >> addressed. If you believe this e-mail was sent to you in >> error and >> the e-mail >> contains patient information, please contact the >> Partners >> Compliance HelpLine at >> >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the >> e-mail was >> sent to >> you in error >> but does not contain patient information, please >> contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> <mailto:[email protected].**edu <[email protected]>> >> <mailto:[email protected].**edu <[email protected]> >> <mailto:[email protected].**edu <[email protected]>>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 >> <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> >> <http://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> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> <mailto:[email protected].**edu<[email protected]> >> > >> 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> >> >> <http://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> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > Phone Number: 617-724-2358 Fax: 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> > >
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