Oh, right, the nuisance regressors are given a separate regressor for
each run. I had forgotten!
On 07/17/2013 04:55 PM, Joseph Dien wrote:
>
> On Jul 17, 2013, at 4:50 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>>
>> On 07/17/2013 04:48 PM, Joseph Dien wrote:
>>> The sing
It's a little complicated. Basically there were eight runs, comprising four
conditions (me, we, you1, you2) each with two adjoining runs. For the
analysis, I merged each of the pairs into a single run and added a nuisance
regressor to account for the difference in run means. There were a tota
It's a boxcar design so 20.265.
mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh
-fwhm 5 -event-related -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2
-refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7
-tpexclude tpexclude.dat
On Jul 17, 2013
then I get on the order of .02% difference between the contrasted conditions.
The run mean values are in my expected ballpark of about 100 or so.
The condition betas are just very very small.
Or perhaps this is typical of FSFAST analyses?
On Jul 17, 2013, at 2:00 PM, Douglas N Greve wrote:
>
>
I implemented the ROI percent signal change formula following the MarsBaR FAQ
(http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too
small (on the order of .0002%). Basically the formula is the (beta * peak
absolute value of the canonical HRF regressor * 100)/(run mean).
Oh, right, it is probably not there for subcortical. I don't know what I
would have to do to write it out. It won't be something that happens
before I get back from HBM. Can you remind me after HBM?
doug
On 05/31/2013 04:44 PM, Joseph Dien wrote:
> It looks like the corrected vertex p-values
>
It looks like the corrected vertex p-values (ex:
cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh
and rh spaces. For the subcortical volume-based analysis I don't see the
corresponding corrected voxel p-values being available?
On May 31, 2013, at 2:46 PM, Joseph Die
On 05/31/2013 02:45 PM, Joseph Dien wrote:
>
> On May 31, 2013, at 12:09 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>>
>> On 05/30/2013 04:37 PM, Joseph Dien wrote:
>>> Just to make sure I'm doing this right, I'm going to summarize what
>>> I've taken away from your answers
On May 31, 2013, at 12:11 PM, Douglas N Greve wrote:
>
> On 05/31/2013 01:49 AM, Joseph Dien wrote:
>> I was able to make more progress so I'm mostly good at this point but
>> I have a remaining question:
>>
>> I assume the contents of sig.nii.gz (which I assume are the vertex
>> p-values) a
On May 31, 2013, at 12:09 PM, Douglas N Greve wrote:
>
> On 05/30/2013 04:37 PM, Joseph Dien wrote:
>> Just to make sure I'm doing this right, I'm going to summarize what
>> I've taken away from your answers and to ask some new questions. In
>> order to present the results, I need two things:
On 05/31/2013 01:49 AM, Joseph Dien wrote:
> I was able to make more progress so I'm mostly good at this point but
> I have a remaining question:
>
> I assume the contents of sig.nii.gz (which I assume are the vertex
> p-values) are not FWE corrected. Is it possible to get FWE-corrected
> vert
On 05/30/2013 04:37 PM, Joseph Dien wrote:
> Just to make sure I'm doing this right, I'm going to summarize what
> I've taken away from your answers and to ask some new questions. In
> order to present the results, I need two things:
>
> 1) A set of histograms (with error bars) for each cluster
I was able to make more progress so I'm mostly good at this point but I have a
remaining question:
I assume the contents of sig.nii.gz (which I assume are the vertex p-values)
are not FWE corrected. Is it possible to get FWE-corrected vertex p-values?
Or are only clusterwise corrections avail
Just to make sure I'm doing this right, I'm going to summarize what I've taken
away from your answers and to ask some new questions. In order to present the
results, I need two things:
1) A set of histograms (with error bars) for each cluster figure to show the %
signal change for each of the f
On 5/29/13 10:42 PM, Joseph Dien wrote:
On May 29, 2013, at 11:40 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
Hi Joe,
On 05/29/2013 01:00 AM, Joseph Dien wrote:
I need to extract the beta weights from a cluster identified with
FS-Fast in order to compute percentage signa
On May 29, 2013, at 11:40 AM, Douglas N Greve wrote:
> Hi Joe,
>
> On 05/29/2013 01:00 AM, Joseph Dien wrote:
>> I need to extract the beta weights from a cluster identified with
>> FS-Fast in order to compute percentage signal change.
>>
>> 1) I see a file called beta.nii.gz that appears to
Hi Joe,
On 05/29/2013 01:00 AM, Joseph Dien wrote:
> I need to extract the beta weights from a cluster identified with
> FS-Fast in order to compute percentage signal change.
>
> 1) I see a file called beta.nii.gz that appears to have the beta
> weight information. It has a four dimensional str
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