Mark,

isn't this what the stats/sigmasquareds volume is? btw, the avwmaths cmd 
below will under estimate the variance slightly as it will take into 
accnt the proper DOF.

doug

Mark Jenkinson wrote:

> Hi,
>
> You can calculate the voxel-wise variance from the 4D residuals
> by using
>   avwmaths++ res4d -Tstd -sqr variance_map
>
> That should be what you want.
>
> All the best,
>     Mark
>
>
>
> On 5 Jan 2007, at 19:55, Clare Kelly wrote:
>
>> Thanks Michael, I had seen that but what I was thinking of was a 2D
>> file that gives one value for the error variance for each voxel -  in
>> the same way that the varcope images provide a measure of how much
>> signal is not accounted for by one particular EV - how do I calculate
>> this for the whole model... or does that not make sense?!?
>>
>> Thanks!
>> Clare
>>
>> On 1/5/07, Michael Hanke <[log in to unmask]> wrote:
>>
>>> Hi,
>>>
>>> On Fri, Jan 05, 2007 at 06:30:44PM +0000, Clare Kelly wrote:
>>> > Hi all,
>>> >
>>> > I apologise if this is a really basic question but I can't seem  
>>> to find the answer I'm looking for in the
>>> > archive.
>>> >
>>> > I want to calculate the residuals for a particular model that  
>>> included 4 task regressors plus their
>>> > temporal derivatives, 8 nuisance regressors, and 6 motion  
>>> parameters, as I want to compare the
>>> > residuals between different models with different numbers of  
>>> regressors.
>>> >
>>> > I understand that each varcope gives me the error related to  that 
>>> particular EV, but I'm not clear on
>>> > how I combine them - I have looked at section 14.5 of the  Jezzard 
>>> et al. book but I still don't know
>>> > what to do.
>>> FEAT can output the residuals for you (no need to calculate  anything).
>>> In fact it always stores them to disk, but deletes them at the end of
>>> the analysis. Just look at the end of you design.fsf file and you'll
>>> see:
>>>
>>> # Delete GLM residuals?
>>> set fmri(cleanup_residuals_yn) 1
>>>
>>> Change this default into:
>>>
>>> # Delete GLM residuals?
>>> set fmri(cleanup_residuals_yn) 0
>>>
>>> and you'll find a res4d.nii.gz (or whatever suffix) in the stats
>>> directory when Feat is finished.
>>>
>>> HTH.
>>>
>>>
>>> Cheers,
>>>
>>> Michael
>>>
>>>
>>>
>>> -- 
>>> GPG key:  1024D/3144BE0F Michael Hanke
>>> http://apsy.gse.uni-magdeburg.de/hanke
>>> ICQ: 48230050
>>>
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[log in to unmask]
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Fax: 617-726-7422

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