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SPM  February 2011

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Subject:

Re: EEG significant clusters outside the MIP glass brain

From:

Vladimir Litvak <[log in to unmask]>

Reply-To:

Vladimir Litvak <[log in to unmask]>

Date:

Tue, 15 Feb 2011 11:20:54 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (118 lines)

Dear Muhammad,

It looks like the analysis you are doing is at the sensor level, but
you use a brain mask. This does not make sense. In your original
message you said that you are getting clusters outside the brain so I
assumed that you are talking about source images. If you are doing
sensor level analysis and you smooth your images you can possibly get
clusters extending outside the scalp. To avoid that you can generate a
mask using Other/Mask Images. You should provide an original
unsmoothed image as input.

Best,

Vladimir

On Tue, Feb 15, 2011 at 2:52 AM, MP <[log in to unmask]> wrote:
> hi Michael,
> The mask looks fine to me. Could it be due to different dimensions of the
> mask and the stat map?
> - M
>
> On Mon, Feb 14, 2011 at 9:39 PM, Michael T Rubens <[log in to unmask]>
> wrote:
>>
>> no idea, did you look at the mask to see what it looks like?
>>
>> what kind of threshold/correction are you using? if you're using a cluster
>> based threshold like friston's cluster fdr then it could be that off brain
>> stuff is inflating clusters that don't pass correction with the mask.
>>
>> Cheers,
>> Michael
>>
>> On Mon, Feb 14, 2011 at 6:27 PM, MP <[log in to unmask]> wrote:
>>>
>>> Thanks Michael, but even then the results ARE very different when I use
>>> the "inclusive" iskull.nii  mask on stat map. See attached.
>>> What do you think is going on?
>>>
>>> On Mon, Feb 14, 2011 at 9:09 PM, Michael T Rubens <[log in to unmask]>
>>> wrote:
>>>>
>>>> that is not right, the results should change due to the mask. Why don't
>>>> you just run the analysis and mask out the resulting stat map. You're
>>>> obviously not interested in anything off the brain (i.e., noise) anyway, so
>>>> its valid.
>>>>
>>>> Cheers,
>>>> Michael
>>>>
>>>> On Mon, Feb 14, 2011 at 5:25 PM, MP <[log in to unmask]> wrote:
>>>>>
>>>>> Hello Vladimir,
>>>>> I tried to use the inner skull mask as you suggested to avoid getting
>>>>> significant cluster outside the glass brain, but it is drastically changing
>>>>> the results. Attached the figures of results with and without applying the
>>>>> mask. Could you please tell me if I am doing something wrong here?
>>>>> P.S. I include the iskull mask as an implicit mask in the flexible
>>>>> factorial design.
>>>>> Thanks
>>>>> - Muhammad
>>>>>
>>>>> On Fri, Dec 31, 2010 at 12:03 AM, <[log in to unmask]> wrote:
>>>>>>
>>>>>> Dear Muhammad,
>>>>>>
>>>>>> Threshold masking will not necessarily work. It depends whether the
>>>>>> values outside the brain are really low. You can use an explicit inner skull
>>>>>> mask. There should be one in EEGTemplates as far as I remember or you can
>>>>>> make your own.
>>>>>>
>>>>>> You can either re-run your stats or use small volume correction for
>>>>>> inner skull but the latter will not fix the graphics.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Vladimir
>>>>>>
>>>>>> Sent from my BlackBerry® smartphone from orange
>>>>>>
>>>>>> ________________________________
>>>>>> From: MP <[log in to unmask]>
>>>>>> Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
>>>>>> Date: Thu, 30 Dec 2010 21:33:40 -0500
>>>>>> To: <[log in to unmask]>
>>>>>> ReplyTo: MP <[log in to unmask]>
>>>>>> Subject: [SPM] EEG significant clusters outside the MIP glass brain
>>>>>> Hello all,
>>>>>> I am doing EEG analysis using SPM8 and while viewing the results, I
>>>>>> see that some of the significant clusters appear outside the brain. I
>>>>>> understand that it could be due to smoothing of the images, but is there a
>>>>>> way to restrict these clusters inside the MIP? I think Threshold masking may
>>>>>> be the way to go, but I am not sure what threshold value to use?
>>>>>> If indeed threshold masking is the way to go, would I need to re-do
>>>>>> all the analyses?
>>>>>> Any help would be much appreciated.
>>>>>> Thanks
>>>>>> - Muhammad
>>>>
>>>>
>>>>
>>>> --
>>>> Research Associate
>>>> Gazzaley Lab
>>>> Department of Neurology
>>>> University of California, San Francisco
>>>
>>
>>
>>
>> --
>> Research Associate
>> Gazzaley Lab
>> Department of Neurology
>> University of California, San Francisco
>
>

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