Hi,
Just provide the relevant input information to cluster (e.g. --dlh, --volume and --pthresh)
and ask for the --opvals output. You can also get the p-value information from the
table that it produces.
All the best,
Mark
On 7 Jun 2012, at 00:24, Diederick Stoffers wrote:
> Hi Mark,
>
> One more question; I would much prefer to have FSL calculate the FWE corrected probability. I have the correct masks and know the spatial smoothness of the data (10 mm FWHM). How would I go about using FSL to do cluster statistics on the tstat maps that were provided to me?
>
> Many thanks,
>
> Diederick
>
> On Jun 6, 2012, at 4:28 PM, Diederick Stoffers wrote:
>
>> Thanks Mark! Didn't grasp the --osize option from cluster's info, that will save me some scripting.
>>
>> The spm's and cluster sizes were provided to me by an expert AFNI user, not something I would normally use in my FSL-based analysis.
>>
>> Cheers,
>>
>> Diederick
>>
>> On Jun 6, 2012, at 3:41 PM, Mark Jenkinson wrote:
>>
>>> Dear Diederick,
>>>
>>> We don't normally specify the size as a threshold, but rather use the FWE corrected probability.
>>> It is related to size though, and so if you have the size values (and they are validly calculated)
>>> then you can do it that way around. In that case you would use the --osize option (which puts
>>> a value into each voxel in a cluster that is equal to the cluster's size) and then use fslmaths
>>> with the -thr set to your cluster size threshold.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 6 Jun 2012, at 20:41, Diederick Stoffers wrote:
>>>
>>>> Hi all,
>>>>
>>>> I have a collection of Z-maps and a table with cluster sizes needed to survive FWE-correction at different combinations of uncorrected and corrected thresholds. To my surprise it seems there is no easy way to output masks for a set cluster size threshold; the only I see is to combine the output from the cluster command, awk and fslmaths to get these masks. Am I correct or is there an easier way?
>>>>
>>>> Cheers,
>>>>
>>>> Diederick
>>
>
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