fixing conflict

expandBrainMask.m

+% 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
+
+% CT_post = NiftiMod('seeg_electrode_additional_tryout_high_threshold_2.nii.gz');
+% Brain_mask = NiftiMod('brain_mask.nii.gz');
+brainMaskImg = Brain_mask.img;
+
+structEl = strel('sphere', 3);
+expndBrainMask = imdilate(brainMaskImg, structEl);
+
+isosurface(expndBrainMask);
\ No newline at end of file

sEEG_Segmentation_Script.m

 % PCA
-
 %CT_post = NiftiMod('Seeg_chinese_1_before_final.nii');
 %CT_post = NiftiMod('seeg_seg_bul_inside_binary.nii');
 CT_post = NiftiMod('seeg_electrode_additional_tryout_high_threshold_2.nii.gz');
@@ -28,6 +27,19 @@ MAXVOXELNUMBER_CONTACTS = 150;
 MINVOXELNUMBER_HEAD = 200;
 MAXVOXELNUMBER_HEAD = 2000;
 
+%% TODO: rename brainmask files in all folders to not get them confused!!!
+% 
+% CT_post = NiftiMod('seeg_electrode_additional_tryout_high_threshold_2.nii.gz');
+% Brain_mask = NiftiMod('brain_mask.nii.gz');
+% Brain_mask_img = Brain_mask.img;
+% 
+% bm = bwconncomp(Brain_mask_img,26);
+% 
+% bmProps = regionprops(bm, Brain_mask.img, 'Area', 'PixelIdxList', 'PixelList', 'PixelValues', 'BoundingBox', 'Centroid');
+% [areas, idxs] = sort([bmProps.Area], 'descend'); % sort by size
+% 
+% bm_centroid = bmProps(idxs(:,1)).Centroid
+
 %% TODO: find some solution for electrodes, where the contacts regions are "melted" together and no seperate
 %% regions and head are defined