Dear Stephen,
Thanks!
Bests,
Matthias
Stephen Smith wrote:
> Hi - it is not _too bad_ to run smoothest on the zstat map (as opposed
> to the residuals) - that's what easythresh does. However you should
> definitely not run it on the thresholded zstat map.
>
> You don't have to feed already-thresholded zstat maps into cluster -
> you can have cluster do the thresholding for you - see the list of
> various options.
>
> Cheers.
>
>
> On 6 May 2010, at 16:14, Matthias Ekman wrote:
>
>> Dear Experts,
>>
>> I want to cluster some self generated zstat map using fsls 'cluster'
>> tool.
>> I am aware of the fact that its not recommended to use smoothest in
>> this case (because zstats also contains signal; and I want an estimate
>> of the smoothness of the noise), but this might be the only way to go
>> for me here.
>>
>> Since 'cluster' uses a thresholded zstat map as input ("-i
>> thresh_zstat1"):
>> $ cluster -i thresh_zstat1 -t 3.09 -p 0.05 -d 0.118826 --volume=280012
>> --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --mm
>> --olmax=lmax_zstat1_std.txt > cluster_zstat1_std.txt
>>
>> I would like to ask if you would recommend to use 'smoothest' also
>> with the thresholded zstat map (or with the original zmap)?
>> In my case this makes a huge difference:
>>
>> # > smoothest with original zmap:
>> $ smoothest -z zstat -m merged_mask
>>
>> DLH 0.118826
>> VOLUME 280012
>> RESELS 38.8524
>>
>> # > smoothest with thresholded zmap:
>> $ smoothest -z thresh_zstat -m merged_mask
>>
>> DLH 0.865882
>> VOLUME 280012
>> RESELS 5.33175
>>
>>
>> Kind regards,
>> Matthias
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] <mailto:[log in to unmask]>
> http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/%7Esteve>
> ---------------------------------------------------------------------------
>
>
>
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