From ea17730b7c99b766d0e725e87cd20f59b4505cbd Mon Sep 17 00:00:00 2001
From: Andreas <27815260+adhusch@users.noreply.github.com>
Date: Fri, 27 Apr 2018 17:11:13 +0200
Subject: [PATCH] Towards 0 failures..

---
 src/Functions/extractBrainConvHull.m        | 9 ++++++---
 src/Functions/extractElectrodePointclouds.m | 2 +-
 src/PaCER.m                                 | 2 +-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/Functions/extractBrainConvHull.m b/src/Functions/extractBrainConvHull.m
index 3d37437..cfb0b0c 100644
--- a/src/Functions/extractBrainConvHull.m
+++ b/src/Functions/extractBrainConvHull.m
@@ -29,7 +29,8 @@
 ctIso = niiCT.img; % = downsampleImage(niiCT.img, niiCT.voxsize, niiCT.voxdim);
 
 % threshold
-threImg = (ctIso > LOWER_CT_BRAIN_THRESHOLD & ctIso < UPPER_CT_BRAIN_THRESHOLD);
+ctIsoMedFilt =  medfilt3(ctIso);
+threImg = (ctIsoMedFilt > LOWER_CT_BRAIN_THRESHOLD & ctIsoMedFilt < UPPER_CT_BRAIN_THRESHOLD);
 %threImg = reshape(threImg,niiCT.voxdim');
  [xx,yy,zz] = ndgrid(-2:2);
 structEle = sqrt(xx.^2 + yy.^2 + zz.^2) <= 2.5 / sqrt(max(niiCT.voxsize));
@@ -38,10 +39,12 @@
 %G = gpuArray(structure); % if we have CUDA..
 
 % morphology
+%threImg = medfilt3(threImg);
 morphImg = imopen(threImg,structEle);
 morphFaction = sum(morphImg(:)) / numel(morphImg);
-if(morphFaction < 0.05 || morphFaction > 0.3)
+if(morphFaction < 0.06 || morphFaction > 0.3)
     warning('Uncommon fraction of CT data in threshold range (15-60 HU). Trying to compensate. Make sure to use "soft tissue" reconstruction filters for the CT (e.g. J30 kernel) if this fails. ')
+    threImg = medfilt3(threImg);
     morphImg = imclose(threImg,structEle); %maybe we have a super noise brain tissue image, thus to CLOSE instead of open first
     morphImg = imerode(morphImg,structEle); % due to the closing all masks will enlarge, i.e. the brain mask might cover the ckull, thus we have to shrink it at the very end again
 end 
@@ -63,7 +66,7 @@
 convHullBrainMask = false(size(roughBrainMask));
 maskedCT = ctIso;
 maskedCT(~roughBrainMask) = NaN; %threshold the roughBrainMask again to make sure no skull is contained due to morphology
-roughBrainMask = (maskedCT > LOWER_CT_BRAIN_THRESHOLD & maskedCT < UPPER_CT_BRAIN_THRESHOLD);
+roughBrainMask = (maskedCT > LOWER_CT_BRAIN_THRESHOLD & maskedCT < UPPER_CT_BRAIN_THRESHOLD); %TODO check if removable
 for i=1:size(roughBrainMask,3)
     convHullBrainMask(:,:,i) = bwconvhull(roughBrainMask(:,:,i));
     roughBrainMask(:,:,i) = imfill(roughBrainMask(:,:,i), 'holes');
diff --git a/src/Functions/extractElectrodePointclouds.m b/src/Functions/extractElectrodePointclouds.m
index 173efb0..d044522 100644
--- a/src/Functions/extractElectrodePointclouds.m
+++ b/src/Functions/extractElectrodePointclouds.m
@@ -8,7 +8,7 @@
 
 function [elecsPointcloudStruct, brainMask] = extractElectrodePointclouds(niiCT, varargin)
     % CONSTANTS
-    LAMBDA_1 = 30; % 
+    LAMBDA_1 = 25;  % elec latent space length [mm]
 
     %% Optional Arguments and Default Values
     argParser = inputParser();
diff --git a/src/PaCER.m b/src/PaCER.m
index 1d67ff1..c01868b 100644
--- a/src/PaCER.m
+++ b/src/PaCER.m
@@ -32,7 +32,7 @@
    args.contactDetectionMethod = 'contactAreaCenter'; 
 end
 %% Checks
-if(~isa(niiCT, 'NiftiMod'))
+if(~isa(niiCT, 'NiftiMod') && ~isa(niiCT, 'NiftiModSPM') )
     disp('First parameter is not a nifti object. Intrepretating as filename and tring to load a nifti file with that name from disk...');
     niiCT = NiftiMod(niiCT);
 end