On Wed, Aug 10, 2011 at 2:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

You can't do that with FSFAST. You can do something like that with mri_glmfit, something like:

mri_glmfit --y fmc.nii --qa --glmdir qa.glm --save-yhat

This will detrend the time series (removing mean, linear, and quadratic trends). With --save-yhat, one of the outputs will be yhat.mgh (the detrended time series). If you have a task, the task will still be in there.

doug

Yang Liu wrote:

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 <mailto: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>

<mailto: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>>
<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:

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>>>
<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
<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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