On 03/24/2016 07:37 PM, Joseph Dien wrote:
> Doug, I see now what your concern was with just adjusting the beta
> weights. Since FSFAST is using a pseudo-mixed effects model, there is
> also a need to pass the cesvar statistics up to the second level. How
> that might accommodate the
Doug, I see now what your concern was with just adjusting the beta weights.
Since FSFAST is using a pseudo-mixed effects model, there is also a need to
pass the cesvar statistics up to the second level. How that might accommodate
the derivative boost computation is not straightforward to me.
I did more digging around and came up with a procedure. Please let me know if
it would cause any problems.
Looking at the contents of the X.mat files (which contain the predictors), it
appears that the betas are indeed arranged as c1 d1 c2 d2…
I also found that isxconcat-sess requires the
oh duh! Sorry, wasn’t thinking clearly.
Okay, I see how to generate the betas now. I don’t even need to mess with the
mkcontrast-sess command.
I just run selxavg3-sess with the -no-con-ok flag.
With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex.
With spmhrf 1 I generated
The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
On 03/13/2016 10:29 PM, Joseph Dien wrote:
> After a long break, back to this…
>
> My goal is still to get the betas for the first and maybe second spm
> hrf so I can calculate a Calhoun derivative boost measure.
>
> As a first
After a long break, back to this…
My goal is still to get the betas for the first and maybe second spm hrf so I
can calculate a Calhoun derivative boost measure.
As a first step I ran:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5
-event-related -paradigm
I'm thinking of generating a modified beta.nii.gz file where the primary betas
have been replaced with the Calhoun et al (2004) derivative boost measure.
What do you think? Also, please note my question below about the second
derivative as it is causing me concern about my analysis. Thanks!
Sorry, not following what you are suggesting?
I want the second derivative for calculating the Calhoun et al 2004 derivative
boost measure.
My understanding is that to the extent that the BOLD signal deviates from the
canonical hrf, the amplitude of the primary regressor will be attenuated and
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you
mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
On 07/10/2013 01:29 PM, Joseph Dien wrote:
Sorry, not following what you are
On 07/09/2013 04:11 PM, Joseph Dien wrote:
Hi,
I have a question about how mkcontrast-sess works. I ran an
analysis using the mkanalysis-sess option spmhrf 2 so there are three
regressors for each predictor, the primary, the latency, and the
dispersion. When specifying the contrast
Hi,
I have a question about how mkcontrast-sess works. I ran an analysis using
the mkanalysis-sess option spmhrf 2 so there are three regressors for each
predictor, the primary, the latency, and the dispersion. When specifying the
contrast weights for mkcontrast-sess, the documentation
Thanks for the quick response! So if I wanted to use the Calhoun 2004
approach, I should be able to use the Steffener 2010 correction to address the
violation of the assumption that the regressors were standardized and generate
a new beta.nii.gz file where the primary beta values have been
I tried correlations and the 2nd derivative is definitely not orthogonal.
corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1. -0. -0.5427
-0.1. -0.0298
-0.5427 -0.02981.
I looked at the regressors that SPM generates for the same data:
ans =
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