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Hi Anderson, But is there a way to calculate p values and size of each tracts in clusters from whole brain analysis and not from specific mask. Thank you, Archana # Hi Archana, # # There's one big cluster that involves multiple structures. It doesn't make # much sense to break down this cluster into sub-clusters (?) and try to # obtain a p-value for each after randomise has already run. Instead, if # you'd like to run a test on a given structure, define a mask for that # structure, and give it to randomise with the option "-m". # # All the best, # # Anderson # # # On 16 March 2015 at 05:19, Archana Malagi <[log in to unmask]> wrote: # #> ---------------------------- Original Message #> ---------------------------- #> Subject: Re: [FSL] How to extract cluster size and p values #> From: [log in to unmask] #> Date: Mon, March 16, 2015 10:31 am #> To: [log in to unmask] #> -------------------------------------------------------------------------- #> #> Hi Rosalia and Eduardo, #> #> As discussed, i applied threshold 0.96 , 0.97 while using cluster #> command #> and also attached snapshot of tbss results : #> #> threshold 0.96 #> #> Cluster Index Voxels MAX MAX X (vox) MAX Y (vox) MAX Z #> (vox) COG X #> (vox) COG Y (vox) COG Z (vox) #> 1 32483 0.999 70 150 105 84.3 126 94.2 #> #> and threshold 0.97 #> #> Cluster Index Voxels MAX MAX X (vox) MAX Y (vox) MAX Z #> (vox) COG X #> (vox) COG Y (vox) COG Z (vox) #> 1 31264 0.999 70 150 105 84.1 126 94.2 #> #> #> Results of atlasquery with threshold: 0.96 and 0.97 gives same results. #> #> #> As a result, it gives only one cluster for both the thresholds and most #> of #> cluster the lies is in right hemisphere. #> #> Thank you, #> #> Archana #> #