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Hi again, in searching for an alternative method to cluster the output from randomize i came across the following commands. However, when I look at the command: fslmaths grot_tfce_corrp_tstat1 -thr 0.95 -bin -mul grot_tstat1 grot_thresh_tstat1 it is not clear where I get the input file grot from? I assume it is from running: fslmaths tbss_tfce_corrp_tstat1 -thr 0.95 grot_tfce_corrp_tstat1? If so, when I run the above command I get an error message “cannot open volume tbss_tfce_corrp_tstat1 for reading” I have checked this file and it opens in fslview. What am I missing? Thank you again, ~meisan > On Aug 11, 2016, at 12:23 PM, Meisan Brown-Lum <[log in to unmask]> wrote: > > Dear FSL team, > > To correlate TBSS findings with behavioural data, I am looking to extract FA values from clusters of significance after running the TBSS randomize tool. From viewing the corrp_tstat1 output in fslveiw I see greater FA results in the control vs patient group that are quite dispersed throughout the brain - so I assume that there should be many clusters of significance. > > To quantify these results, I then used the following command: cluster -i tbss_tfce_corrp_tstat1.nii.gz -t 0.95 --mm > cluster_t1_95.output > > Of concern, I only get 1 cluster in the output and it is very large (many voxels) and anatomically does not make sense. Is there a way to break up the cluster and extract peak FA values from them? > > Thank you kindly for your guidance on this, > ~meisan