From 5d8edf0bf319e5ddc4d778b0e6e19eaa9afab077 Mon Sep 17 00:00:00 2001
From: bacaron <bacaron@imail.iu.edu>
Date: Fri, 24 Feb 2017 16:50:30 -0500
Subject: [PATCH] Update and rename 05_make_wm_mask.m to zero5_make_wm_mask.m

changed name, added notes and header
---
 Concussion/05_make_wm_mask.m    | 37 ---------------------------------
 Concussion/zero5_make_wm_mask.m | 37 +++++++++++++++++++++++++++++++++
 2 files changed, 37 insertions(+), 37 deletions(-)
 delete mode 100644 Concussion/05_make_wm_mask.m
 create mode 100644 Concussion/zero5_make_wm_mask.m

diff --git a/Concussion/05_make_wm_mask.m b/Concussion/05_make_wm_mask.m
deleted file mode 100644
index 3750c8b..0000000
--- a/Concussion/05_make_wm_mask.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%
-% This script makes the white-matter mask used to track the connectomes in
-% Caiafa and Pestilli Manuscript.
-%
-% 
-% Copyright Franco Pestilli (c) Indiana University, 2016; 
-% 2017 adapted by Brad Caron 
-
-% Get the base directory for the data
-anatomypath = '/N/dc2/projects/lifebid/Concussion/concussion_test';
-subjects = {'1_002', '1_003'};
-
-for isbj = 1:length(subjects)
-    wmMaskFile = fullfile(anatomypath,subjects{isbj},'diffusion_data', '1000', 'Anatomy', 'wm_mask.nii.gz');
-    
-    fs_wm = fullfile(anatomypath,subjects{isbj},'diffusion_directory', 'Anatomy', 't1_acpc_bet.nii.gz');
-    fprintf('\n loading %s \n',fs_wm);
-    wm = niftiRead(fs_wm);
-    wm.fname = wmMaskFile;
-    invals  = [2 41 16 17 28 60 51 53 12 52 13 18 54 50 11 251 252 253 254 255 10 49 46 7];
-    origvals = unique(wm.data(:));
-    fprintf('\n[%s] Converting voxels... ',mfilename);
-    wmCounter=0;noWMCounter=0;
-    for ii = 1:length(origvals);
-        if any(origvals(ii) == invals)
-            wm.data( wm.data == origvals(ii) ) = 1;
-            wmCounter=wmCounter+1;
-        else            
-            wm.data( wm.data == origvals(ii) ) = 0;
-            noWMCounter = noWMCounter + 1;
-        end
-    end
-    fprintf('converted %i regions to White-matter (%i regions left outside of WM)\n\n',wmCounter,noWMCounter);
-    niftiWrite(wm);
-end
-
-end % Main function
diff --git a/Concussion/zero5_make_wm_mask.m b/Concussion/zero5_make_wm_mask.m
new file mode 100644
index 0000000..74599f6
--- /dev/null
+++ b/Concussion/zero5_make_wm_mask.m
@@ -0,0 +1,37 @@
+% This script makes the white-matter mask used to track the connectomes in
+% Caiafa and Pestilli Manuscript.
+%
+% Input is the parcellated and segmented white matter mask from freesurfer segmentation 
+% (github.com/brain-life/pestillilab_projects/Concussion/freesurfer_segmentation), subject (subj), and anatomy 
+% directory (anatomypath).
+%
+% Output will be wmMask.nii.gz file.  This will be used in mrtrix tracking 
+% (github.com/brain-life/pestillilab_projects/zero6_ensemble_tractography).
+%
+% 2017 Brad Caron Indiana University, Pestilli Lab 
+
+% Get the base directory for the data; edit for your data and file structure
+anatomypath = '/N/dc2/projects/lifebid/Concussion/concussion_test';
+subjects = '1_005';
+
+wmMaskFile = fullfile(anatomypath,subjects{isbj},'diffusion_data', '1000', 'Anatomy', 'wmMask.nii.gz');    
+fs_wm = fullfile(anatomypath,subjects{isbj},'diffusion_directory', 'Anatomy', 'aparc+aseg.nii.gz');
+fprintf('\n loading %s \n',fs_wm);
+wm = niftiRead(fs_wm);
+wm.fname = wmMaskFile;
+invals  = [2 41 16 17 28 60 51 53 12 52 13 18 54 50 11 251 252 253 254 255 10 49 46 7];
+origvals = unique(wm.data(:));
+fprintf('\n[%s] Converting voxels... ',mfilename);
+wmCounter=0;noWMCounter=0;
+for ii = 1:length(origvals);
+    if any(origvals(ii) == invals)
+    wm.data( wm.data == origvals(ii) ) = 1;
+    wmCounter=wmCounter+1;
+        else
+        wm.data( wm.data == origvals(ii) ) = 0;
+        noWMCounter = noWMCounter + 1;
+        end
+    end
+    fprintf('converted %i regions to White-matter (%i regions left outside of WM)\n\n',wmCounter,noWMCounter);
+    niftiWrite(wm);
+end