Hey Anderson,

Thank you for your prompt reply. Just to reconfirm : Step 1 : use fdr command (fdr -i input image -m mask -q 0.05 -a p val image ) and then Step 2 : use cluster command (cluster - i p val image -t threshold? --oindex clusterindexffile --olmax clustelocalmaxima.txt )

Does these commands make sense? Moreover, what threshold should I take while using the cluster command.?
Thanks

Sincerely,
Sankalp 


Sankalp Tikoo,
Doctoral student -La Sapienza, University of Rome

Human Neuroscience Department

v.le dell'Università 3000185 Rome-Italy 

email:[log in to unmask]



On Mon, Sep 16, 2019 at 3:53 AM Anderson M. Winkler <[log in to unmask]> wrote:
Hi Sankalp,

Yes, I think the option -a will allow you to save the adjusted p-values. You can then use the command "cluster" to see the values within each cluster (since each cluster has all voxels with the same p-value, the peak value within the cluster is the number that you want.

All the best,

Anderson


On Thu, 12 Sep 2019 at 09:00, sankalp tikoo <[log in to unmask]> wrote:
Dear Anderson,

The randomise command in fsl has given me a vox p tstat file and after applying FDR  correction on it I get significant clusters. I wanted to ask , is there any way to extract p values from those significant clusters post FDR correction?

Thanks for your prompt response

--


Sankalp Tikoo,
Doctoral student -La Sapienza, University of Rome

Human Neuroscience Department

v.le dell'Università 3000185 Rome-Italy 

email:[log in to unmask]


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