//WIP added expanding function for the brain mask

need to have this function to threshold the images, so everything outside of the brain except the electrode heads will be removed

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_chinese_1_before_final.nii');
 %CT_post = NiftiMod('seeg_seg_bul_inside_binary.nii');
 
 %% CONSTANTS
@@ -15,6 +15,19 @@ 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