Thanks,
Could I also create my mask as you described and then use this as
'explicit mask' in the 2nd level analysis?
Also, another question regarding the statistical threshold on the
second level analysis:
The default value in the '2nd-level Analysis' is FWE, alpha=0.05.
I don't understand why, at the second level and for a simple t-test,
one would have to perform an error correction.
Should I use an uncorrected error with alpha=0.05 at this step?
[The recommended smoothing for the second level could also be seen as
some error adjustment]
Michael
University of Alabama at Birmingham
On Jun 14, 2009, at 3:57 PM, Helmut Laufs wrote:
> In order to create a mask, you could first select a(ny) normalized
> brain
> with the same dimensions as your normalised con images and perform the
> operation i1>.1 (well, check the gray value of the "black"
> background around
> the actual brain). This will give you a b/w image with the area of
> the brain
> being white (all ones), the background being black (zeros). In a
> next step
> you would chose the latter image (your mask) and your smoothed con
> image and
> perform an i1 and i2 resulting in your smoothed con images with all
> zeros
> around the actual area of the brain with your gray values preserved.
> You
> could do this operation in a single step, I guess. Actually, I have
> not
> checked this, but in principle it should work like this...
>
> Hth,
>
> bw,
>
> HL
>
>
> ----- Original Message -----
> From: "Michael Froelich" <[log in to unmask]>
> To: "Helmut Laufs" <[log in to unmask]>
> Sent: Thursday, June 11, 2009 4:53 PM
> Subject: Re: 2nd-level Smoothing
>
>
>> How do you use imcalc to apply a mask, let's say to the normalized
>> activation map of the second level?
>>
>> Michael
>>
>>
>> On Jun 11, 2009, at 4:44 AM, Helmut Laufs wrote:
>>
>>> Yes, you would. In addtion you may want to use imcalc to apply a
>>> mask
>>> afterwards in order to limit "blobs" to the brain.
>>>
>>> Bw,
>>>
>>> Helmut
>>>
>>> ----- Original Message -----
>>> From: "Michael Froelich" <[log in to unmask]>
>>> Sent: Wednesday, June 10, 2009 10:32 PM
>>> Subject: 2nd-level Smoothing
>>>
>>>
>>> Dear SPM community,
>>>
>>> At the SPM8 refresher course, the question about smoothing was
>>> asked. IN
>>> reply, Dr.
>>> Friston recommended an approximate 6 mm smoothing kernel both for
>>> the
>>> first
>>> and second
>>> level. How is the smoothing accomplished at the second level?
>>>
>>> Would we smooth the ".con" images prior to entering them into a 2nd
>>> level
>>> analysis?
>>>
>>> Michael Froelich
>>>
>>> University of Alabama at Birmingham
>>> Anesthesiology
>>>
>>
>>
>
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