Great, Thank you
To follow up: What is the default setting when I run it without the
GM_mask? I know that the mask outlines the brain but what exactly does
it control in the analysis?
Jeff
On Tue, Aug 17, 2010 at 12:51 PM, Gwenaëlle DOUAUD
<[log in to unmask]> wrote:
> Hi again Jeff,
>
>> Hmm I looked at the html for BET, the
>> template_4D_GM and the GM_mod
>> merg timeseries (both in fslview) and they all look fine.
>> The results
>> are outside of template-4D_GM and GM_mod_merg highlighted
>> regions as
>> well as the MNI152 brain. The MNI152 brain is very closely
>> aligned
>> with the template_4D_GM and the GM_mod_merg files. The
>> protocol I used
>> was as follows:
>>
>> fslvbm_1_bet -N; fslvbm_2_template –n;
>> fslvbm_3_proc –T; cd stats;
>> randomise -i GM_mod_merg_s3 -o Discont_Regress_HAMD -d
>> HAMD.mat -t
>> HAMD.con -e HAMD.grp -T
>> So I think that I am using the correct protocol.
>
> Correct protocol, but incomplete randomise command...
> You need to specify a mask (e.g. GM_mask) in which you have to carry out your stats. If the GM_mask looks ok, then you should be fine (well at least not get anything outside of the brain!).
>
> Cheers,
> Gwenaelle
>
>
>
>> Thank you Gwenaëlle for the quick response,
>> Jeff
>
> --------------------------------------------------------------------
>
> Gwenaëlle Douaud, PhD
>
> FMRIB Centre, University of Oxford
> John Radcliffe Hospital, Headington OX3 9DU Oxford UK
>
> Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
>
> www.fmrib.ox.ac.uk/~douaud
>
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