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Just turn off your implicit mask. You will get some noise off the brain, but
it will solve your problem for now. Its easy to mask off brain voxels after
you normalize. WFU pickatlas can create an MNI brain mask, or there is one
included with FSL that works well too.

Cheers,
Michael

On Thu, Dec 2, 2010 at 12:43 PM, Jana Hanulova <[log in to unmask]>wrote:

> Dear all,
>
> thank you very much for your help - just as you suggested, the mask was
> incorrect (completely black). I checked my settings and I have Threshold
> (none), Implicit mask (yes), Explicit mask (none). Individual subjects' con
> images look OK.
>
> I think that the best solution would be to make an explicit mask, since I
> don't know what and why went wrong with the implicit mask - do you think it
> is a good solution?
>
> Thank you again,
>
> Jana
>
> On Wed, Dec 1, 2010 at 4:18 PM, Michael T Rubens <[log in to unmask]>wrote:
>
>> Matlab creates a mask to limit GLM analysis to in-brain voxels. This is
>> calculated based on a intensity threshold, perhaps it is too stringent. Look
>> at your Mask.img file in the glm output folder and make sure ~isempty(mask).
>>
>> Cheers,
>> Michael
>>
>>
>> On Wed, Dec 1, 2010 at 7:01 AM, Jana Hanulova <[log in to unmask]>wrote:
>>
>>> Hi Erica,
>>>
>>> thank you for your reply! Actually, I am not using a mask. That's why I
>>> was so puzzled by this error message.
>>>
>>> Best,
>>>
>>> Jana
>>>
>>> On Wed, Dec 1, 2010 at 3:05 PM, Erica Julson <[log in to unmask]>wrote:
>>>
>>>> Are you using masking? I've gotten this error before when I created a
>>>> binary mask incorrectly (the mask was just black, so of course there was no
>>>> area for the program to analyse data within). Hope this helps!
>>>>
>>>> -Erica
>>>>
>>>
>>>
>>
>>
>> --
>> Research Associate
>> Gazzaley Lab
>> Department of Neurology
>> University of California, San Francisco
>>
>
>


--
Research Associate
Gazzaley Lab
Department of Neurology
University of California, San Francisco