Cluster based permutation test--Peak coordinates

[yuqing]

HI,

I have used the cluster based permutation test for source level analysis and I am wondering how can I determine the peak MNI coordinates and the cluster size for each significant clusters since I couldn’t find these value reported.

Thank you!

Best,
Yuqing

[Francois]

Right-click on the stat results > File > View file contents, then look for the StatClusters structure, it contains the clusters informations reported by FieldTrip. Look at the FieldTrip documentation for help with these values.

The significance values obtained for each cluster are the same over the entire cluster. If you want the corresponding MNI coordinates, you could find the significant vertices (from pmap field), then average the positions of the vertices in a cluster. You can get the positions from the cortex file, then convert the coordinates to MNI space:
http://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#On_the_hard_drive
http://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#On_the_hard_drive
http://neuroimage.usc.edu/brainstorm/Tutorials/Statistics#On_the_hard_drive

Conversion of coordinates using cs_convert

Dear BrainStorm support team, When I compare the result of the cs_convert command line and the online display of coordinates. In this example, I used Colin27 template brain and 10-20 (19 positions) montage. I guess I missed a step while using the Matlab command but I fail to find out which one. since the coordinates are pretty different. Any input would be helpful, I'm sure. Sorry for the replication of this topic. Best, Gaëlle. [57] [38]

[yuqing]

Problem solved! Thank you for your help!