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FSL  July 2008

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Subject:

Re: thresholding question

From:

Tim Behrens <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 3 Jul 2008 13:53:33 +0100

Content-Type:

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text/plain (79 lines)

help - Tom?


On 3 Jul 2008, at 13:52, Wouwe, Nelleke van wrote:

> Hi Tim,
>
> I am not sure if I understand you correctly: are you saying that I
> cannot use Z-values below 2 because GRF theory is not valid  
> anymore? Why
> is that?
>
> Thanks for your help
> Nelleke
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Tim Behrens
> Sent: 03 July 2008 14:20
> To: [log in to unmask]
> Subject: Re: [FSL] thresholding question
>
> Hi - if you are using Gaussian Random Field theory for your inference
> (i.e. if you are using Flame and not randomise) then it breaks down at
> low Z values (less than about 2).
>
> Cheers
>
> T
>
> On 3 Jul 2008, at 12:56, Nelleke Van Wouwe wrote:
>
>> Hi all,
>>
>> From some previous discussions and Matt Brett's page on cluster
>> thresholding I understand that you chose the z value based on the
>> activation you are looking for;high z for small regions and low Z for
>> big regions (given p<0.05, corrected).
>>
>> I performed a ROI analysis (pre-masked the data with part of the
>> fusiform gyrus and parahippocampal gyrus)with a (corrected) cluster
>> significance threshold of P=0.05 and I tried a very low Z  
>> threshold of
>
>> 1.1.
>> According to the clusterlist below I find a large cluster (232
>> voxels) that
>> is significantly active (P<0.05) with z-max 1.9.
>>
>> I wonder if there are any rules of thumb to determine an  
>> appropriate Z
>
>> threshold (other than the default) and would this z = 1.1 still be a
>> reasonable threshold?
>>
>> Thanks!
>> Nelleke
>>
>> Cluster List
>> Cluster Index Voxels P -log10(P) Z-MAX Z-MAX X (mm) Z-MAX Y (mm) Z-
>> MAX Z
>> (mm) Z-COG X (mm) Z-COG Y (mm) Z-COG Z (mm) COPE-MAX COPE-MAX X
>> (mm) COPE-
>> MAX Y (mm) COPE-MAX Z (mm) COPE-MEAN
>> 5 232 0.0356 1.45 1.83 42 -50 -22 42.7 -47.8 -24.2 193 42 -42 -30 149
>> 4 41 0.039 1.41 2.26 -44 -62 -26 -42.7 -60.2 -25 243 -44 -62 -26 163
>> 3 26 0.0394 1.4 1.68 34 -34 -20 31.5 -35 -19 134 34 -34 -20 107
>> 2 24 0.0394 1.4 1.45 -32 -38 -20 -30.8 -38.3 -18.6 103 -32 -38 -20
>> 87.6
>> 1 1 0.0405 1.39 1.15 24 -48 -6 24 -48 -6 110 24 -48 -6 110
>>
>
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