Hi,
This looks fine but will not allow you to extract meaningful local
maxima within clusters. For that, you should add:
--cope=your_raw_tstat1
which will 'fool' cluster into reporting local maxima in the
'cope' (in fact raw tstat) image as well as other summary information.
Cheers.
On 8 Feb 2008, at 09:17, Soohyun Cho wrote:
> Thank you for your response.
>
> Yes, I used the maxc_tstat as the input to get information about the
> cluster.
> e.g., cluster --in=file_name --thresh=.95 --oindex=name_clusterindex
> --olmax=name_clustermax.txt --osize=name_clustersize >
> name_clustertable.txt --mm
>
> If I want to get the location of the max voxel within a cluster
> thresholded at 1-p>.95 (corrected for cluster extent), I think you
> are suggesting that I use raw tstat as the input?
> In this case, how should I threshold this?
> Can you give me an example syntax that you would use?
>
> Thank you,
>
> Soohyun
>
> On Feb 8, 2008, at 12:28 AM, Steve Smith wrote:
>
>> Hi,
>>
>> On 6 Feb 2008, at 20:37, Soohyun Cho wrote:
>>
>>> Hi,
>>>
>>> I have a question about using the cluster tool on randomise output.
>>> The cluster table gives you the locus of a maximally active voxel.
>>> But don't all voxels within a cluster (identified from randomise)
>>> have the same 1-p value ?
>>
>> Yes, that's right, the cluster has just one p-value. However, if
>> you used the options correctly you may have also fed in the raw
>> tstat image into cluster as wel as the maxc image. Exactly what
>> cluster command did you use?
>>
>> Cheers.
>>
>>> How did the cluster tool pick that Max voxel?
>>>
>>> What is the best way to report the loci of clusters from randomise ?
>>>
>>> Thank you in advance.
>>>
>>> Soohyun.
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>>
>>
>
---------------------------------------------------------------------------
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] http://www.fmrib.ox.ac.uk/~steve
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