External Email - Use Caution
Dear FS experts,
From an statistical map obtained by mri_glmfit-sim, say a cache.th13.abs.sig.masked.mgh map, I would like to list all the significant regions from all clusters in the following intuitive way, for instance:
Supramarginal gyrus: X vertices, X mm^2, peak T-value=X Superior frontal gyrus: Y vertices, Y mm^2, peak T-value=Y ...
That is, the % of significant vertices in the statistical map belonging to each region of the default FS atlas. I know that the cache.th13.abs.sig.cluster.summary file "summarizes" each cluster by a label, but clearly large clusters are made of several different anatomical regions that I would like to report.
In other words, I wonder if there's an easy way to obtain a cluster description report similar to the one provided by the xjview toolbox for voxelbased maps in MNI space.
I know I could probably achieve it by scripting, i.e. but looping through each ROI extracted from an atlas in fsaverage space and applying a mask with the glmfit map and then computing the overlap and such. But probably there's an easir way, or someone has already thought about it. I tried to search about this topic in the archive but failed to find a clear solution, probably I was not searching by the appropriate words.
Thanks a lot in advance,
You can binarize the final cluster map (mri_binarize --i clustermap.mgz --min 0.5 --o bin.clustermap.mgz) Then run mri_segstats --annot fsaverage lh aparc --i bin.clustermap.mgz The mean value will be the fraction of the vertices in the ROI that belongs to (any) significant cluster
On 7/22/2020 9:36 AM, Fred Sampedro wrote:
External Email - Use Caution
Dear FS experts,
From an statistical map obtained by mri_glmfit-sim, say a cache.th13.abs.sig.masked.mgh map, I would like to list all the significant regions from all clusters in the following intuitive way, for instance:
Supramarginal gyrus: X vertices, X mm^2, peak T-value=X Superior frontal gyrus: Y vertices, Y mm^2, peak T-value=Y ...
That is, the % of significant vertices in the statistical map belonging to each region of the default FS atlas. I know that the cache.th13.abs.sig.cluster.summary file "summarizes" each cluster by a label, but clearly large clusters are made of several different anatomical regions that I would like to report.
In other words, I wonder if there's an easy way to obtain a cluster description report similar to the one provided by the xjview toolbox for voxelbased maps in MNI space.
I know I could probably achieve it by scripting, i.e. but looping through each ROI extracted from an atlas in fsaverage space and applying a mask with the glmfit map and then computing the overlap and such. But probably there's an easir way, or someone has already thought about it. I tried to search about this topic in the archive but failed to find a clear solution, probably I was not searching by the appropriate words.
Thanks a lot in advance,
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Fred Sampedro