//WIP added function for Brain Mask

expandBrainMask.m

+function [croppedImg] = expandBrainMask(mskdImg)
+
 % expand the brain mask to threshold the image so we don't get artifacts
 % from everything that it causing them outside of
 % the brain, besides the electrode head candidates
@@ -13,10 +15,11 @@ isosurface(expndBrainMask);
 
 % compute the centroid of the CT to later map the electrode with the
 % expanded brain Mask and get rid of the artefact far away from brain
-stats_CT_post = regionprops(maskedImg);
+stats_CT_post = regionprops(mskdImg);
 centroid_CT_post = stats_CT_post.Centroid;
 
 % compute the centroid of the expanded brain mask  
 stats_expndBrainMask = regionprops(expndBrainMask);
 centroid_expndBrainMask = stats_expndBrainMask.Centroid; 
 
+end
\ No newline at end of file

sEEG_Segmentation_Script.m

@@ -53,6 +53,9 @@ maskedImg = CT_post.img;
 % brainMask = imerode(brainMask,structEle);
 % maskedImg(~(brainMask)) = NaN;
 
+% change accordingly
+croppedImg = expandBrainMask(maskedImg);
+
 cc = bwconncomp(maskedImg,26); % 26 for 3D images
 disp([num2str(cc.NumObjects) ' potential metal components detected within brain.']);