Hi Christine,

Sig = -log(pvalue)

In freeview, the overlay thresholds can be adjusted by clicking ‘Configure’ button (under the Overlay dropdown menu).

For mri_surfcluster (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster),  I think you can try to adjust these options to match freeview: --thmin <>, --thmax <>, --thsign <>, --minarea <>, --no-adjust.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Smith, Christine
Sent: Tuesday, February 21, 2023 6:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] different clusters in mri_surfcluster output versus viewing in Freeview

        External Email - Use Caution        

Hello,

I am getting a mismatch of clusters when we view cluster results in freeview versus ask for a table of the significant clusters. 

I am performing a GLM analysis on Freesurfer to analyze cortical thickness (mri_glmfit). When viewing the significance map with freeview, we set the minimum threshold to 2 for the sig.mgh file. 

We also used the same threshold when creating a summary table of the clusters using mri_surfcluster.  

mri_surfcluster --in {$dir}/visuospatial_MCI_correlation/sig.mgh --hemi left --thmin 2 --thsign pos --minarea 10 --subject fsaverage --surf inflated --annot BN_Atlas --sum {$dir}/visuospatial_MCI_correlation/left.thickness.clustersummary_BN.txt

We were hoping to use the summary text file to identify the clusters on freeview and their characteristics (e.g., size, x, y, z ccordinates). Unfortunately, the regions that we see for both methods don’t match as there are some clusters that we see on the summary text file that we don’t see on freeview and vice versa. How can we make the output of these two methods match up? Note that the issue is not the minimum cluster size in the summary table. When we put that to 1 we still get a mismatch. 

Please note that in the mri_surfcluster program we can indicate that we only want positive results. We don't see a way to do this in freeview or a way for that to affect the p value in freeview. 

Is this possibly the issue? If so, how can we make a picture in freeview that matches our summary table? 

Regards, 

Christine

--

Christine N. Smith, Ph.D.

Research Service, VA San Diego Healthcare System
Department of Psychiatry, University of California San Diego

VA San Diego Healthcare System

VMRF Building 13

3350 La Jolla Village Drive (151A)

San Diego, CA 92161

T: (858) 552-8585; then press *7128