Hi Freesurfers,
I am using R to perform thickness analyses. All subjects are transformed in fsaverage space and all values are placed in a matrix with 327684 columns (163842 for each hemisphere). I put the results back in a surface file (.asc format) and then convert it to a binary Freesurfer format. I then open the files in Freesurfer to view them.
Overall the results make sense and fall in the right places. But I am concerned that some results fall into the corpus callosum, which, if I remember correctly should not have any thickness value, and therefore no results.
Here is a screenshot: [image: Inline image 1]
Can someone help my understand what might be wrong? Or, if this is normal, why I am finding thickness results where there is no thickness?
Is there a way to find label numbers for each vertex in fsaverage space (i.e. list of parcel number for each vertex). This might be useful to exclude certain vertices or compute summery statistics of the results directly in R.
Third question, is it possible to threshold the above map based on minimal cluster area (i.e., in mri_surfcluster). If yes, do I need to prepare a binary file with p-values for thresholding (0-1), or can I use mri_surfcluster with t-score maps (0-Inf)?
Thank you for your help. Dorian
