The value of the vertcies in the OCN is the the cluster number, not a significance. If you are trying to set all non-clusters to 0 (and keep the image the same otherwise), then use the output from the --o flag.

doug

Mandy Nagy wrote:

Hi all,

We ran mri_surfcluster on our group data (we didn't do montecarlo simulations), so we used our .mgh file. We used the -ocn flag to make an output file so we could look at the specific clusters. When we looked at

the data of the ocn file using tksurfer, the most significant cluster wasn't visible at the .05 level (which is the min threshold we specified in the mri_surfcluster). We tried playing with the threshold, but it was

the opposite of what we expected. The most significant clusters disappeared at the lowest threshold but the less significant ones appeared even when we raised the threshold. This happened when we ran the other

hemisphere as well. Do you have any idea how to fix this?

we are using freesurfer v5 subjects_dir: cluster/manoach/milton/subjects

Our commands:

mri_surfcluster --in ./group_analysis/mct_lh/osgm/sig.mgh --hemi lh

--thmin 1.3 --thmax infinity --subject fsaverage --sum ./group_analysis/mct_lh/osgm/mst_v_mct.txt --ocn /cluster/manoach/milton/subjects/group_analysis/mct_lh/osgm/sig.cluster.p05.ocn.mgh

tksurfer fsaverage lh inflated -overlay sig.cluster.p05.ocn.mgh

Thanks in advance!

Best, Mandy Nagy

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