The lh.area in fsaverage is the area of the white surface (as in an individual subject). But the white surface is not like an individual in that many of the folds have been smoothed out (because it is an average). So mri_surfcluster fixes this internally, which is why you see the discrepancy (and the first method is larger than the second). If you want them to be identical, add --no-fix-vertex-area to mri_surfcluster.

On 6/11/2024 10:49 AM, wangzhiwei3233 wrote:

External Email - Use Caution

Dear Freesurfer experts,

I got the area of a cluster by two methods, and found the results were inconstant.

Method 1: During group level analysis, the individual surface was normalized to fsaverage. I exported the cluster area and label file by command mri_surfcluster.

The command ws as followed:

mri_surfcluster --in ./sig.nii.gz --subject fsaverage --hemi lh --centroid --annot aparc --thmin ${thp} --sign ${sigsignTemp} --no-adjust --minarea ${tharea} --sum area${tharea}.${sigsignTemp}${thp_infilename}.cluster.summary --o area${tharea}.${sigsignTemp}${thp_infilename}.cluster.nii.gz --ocn area${tharea}.${sigsignTemp}${thp_infilename}.ocn.nii.gz --olab $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_area${tharea}.${sigsignTemp}${thp_infilename}/label

Method 2: I calculated the cluster area using the label file outputed by mri_surfcluster via the matlab funciton read_curv. I did this to test the method for calculating the area of a label manually drawn by me.

1, I first got the area of each vertex by the command

area = read_curv('../fsaverage/surf/lh.area');

2, I red the IDs of vertices in the label file and added 1

3, I got area values of vertices in the label file and summed them.

I found the areas calculated by the Method2 were much smaller(except one ROI) than the ones exported by mri_surfcluster as shown below.

Area from Method 1：

# ClusterNo Size(mm^2) NVtxs Annot

1 833.94 1999 postcentral

2 578.52 1300 precuneus

3 243.78 463 middletemporal

4 184.72 344 inferiorparietal

5 111.76 292 insula

Area from Method 2：

ClusterNumber Area(mm^2) NVtxs AnotomicalRegion

1 637.39 1999 postcentral

2 480.44 1300 precuneus

3 140.37 463 middletemporal

4 166.33 344 inferiorparietal

5 112.76 292 insula

What's the reason? Where did I do wrong in the method 2?

Thanks.

Best,

zhiwei

--

-----------------------------------------------

Zhiwei Wang（王志伟), Associate Investigator

International Center for Primate Brain Research

Center for Excellence in Brain and Intelligence Technology

Institute of Neuroscience,Chinese Academy of Sciences

Room 215, Building #5, 500 Qiangye Road, Shanghai, 201602,China
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer