I have performed k-means (3) clustering for my seed mask (in patient's space). I would like to now average the clusters across patients in MNI 1mm space. How would I go about doing this?
I used flirt to convert the mask with these commands:
flirt -in clusters3.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out clusters3_str2std.nii.gz -applyxfm -init ../str2std.mat -noresampblur
fslmaths clusters3_str2std.nii.gz -thr 1 clusters3_str2std_thresh.nii.gz
The resulting seed mask has 3 clusters but there are some voxels on the edges that are non-integer values. I was wondering how to prevent or solve this.
Finally how would I now average these clusters in standard space across all 100 subjects?
-AB
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