tiff2nii updates, avoid conflicts with nii_preprocess

rordenlab · Aug 4, 2016 · 5537eca · 5537eca
1 parent 31c3d92
commit 5537eca
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Showing 5 changed files with 38 additions and 7 deletions.
diff --git a/nii_batch12.m → nii_batch12old.m b/nii_batch12.m → nii_batch12old.m
diff --git a/nii_clipeven.m → nii_clipeven_old.m b/nii_clipeven.m → nii_clipeven_old.m
diff --git a/nii_make3d.m b/nii_make3d.m
@@ -4,8 +4,11 @@
 
 inname = fullfile(spm('Dir'),'apriori','brainmask.nii');
 if ~exist(inname, 'file')
-    fprintf('%s error: unable to find image named %s\n', mfilename,inname);
-    return;
+    inname =  fullfile(spm('Dir'),'canonical','avg152T1.nii');
+    if ~exist(inname, 'file')
+        fprintf('%s error: unable to find image named %s\n', mfilename,inname);
+        return;
+    end;
 end
 hdr = spm_vol([inname,',1']); 
 img = spm_read_vols(hdr);

diff --git a/nii_scale_dims.m b/nii_scale_dims.m
@@ -37,9 +37,10 @@ function nii_scale_dims(fnms, scale)
     img = spm_read_vols(hdr);
 
     hdrOut = hdr(1);
-    hdrOut.dim(1) = hdr(1).dim(1)*scale(1);
-    hdrOut.dim(2) = hdr(1).dim(2)*scale(2);
-    hdrOut.dim(3) = hdr(1).dim(3)*scale(3);
+    hdrOut.dim(1) = round(hdr(1).dim(1)*scale(1));
+    hdrOut.dim(2) = round(hdr(1).dim(2)*scale(2));
+    hdrOut.dim(3) = round(hdr(1).dim(3)*scale(3));
+
     hdrOut.mat(1:3, 1:3) = hdr(1).mat(1:3, 1:3)*[1/scale(1) 0 0; 0 1/scale(2) 0; 0 0 1/scale(3)];
     % http://stackoverflow.com/questions/12520152/resizing-3d-matrix-image-in-matlab
     % monotonic, use the methods '*linear', '*cubic', or '*nearest'.

diff --git a/nii_tiff2nii.m b/nii_tiff2nii.m
@@ -1,15 +1,29 @@
-function nii_tiff2nii (files)
+function nii_tiff2nii (files, maskborder, invert)
 %Convert TIFF stack to NIFTI
 % files : (optional) cell string with filenames to convert
+% maskborder : 0=no change, 1=dark, 2=bright
+% invert: 0=no, 1=yes
 %Examples
 % nii_tiff2nii %use GUI
 % nii_tiff2nii({'DWI_STAC.tiff'})
 % nii_tiff2nii({'DWI_STAC.tiff','test.TIF'})
 
 if ~exist('files','var')
-    [files,pth] = uigetfile({'*.tiff;';'*.*'},'Select TIFF Image[s]', 'MultiSelect', 'on'); 
+    [files,pth] = uigetfile({'*.tiff;*.tif';'*.*'},'Select TIFF Image[s]', 'MultiSelect', 'on'); 
     files = strcat(pth, files); %add path to all file names
 end;
+if ~exist('invert','var') 
+    prompt = {'Mask border (0=no, 1=dark, 2=bright):',...
+            'Invert intensity (0=no, 1=yes):'};
+    dlg_title = ['TIFF conversion options'];
+    num_lines = [1 50];
+    def = {'0','0'};
+    answer = inputdlg(prompt,dlg_title,num_lines,def);
+    if isempty(answer), return; end;
+    maskborder = str2num(answer{1});
+    invert = str2num(answer{2});
+end;
+
 files = cellstr(files); %make cellstr nii_tiff2nii({'DWI_STAC.tiff'}) == nii_tiff2nii('DWI_STAC.tiff')
 niiname = fullfile(spm('Dir'),'canonical','avg152T1.nii'); %sample nifti file for header
 if ~exist(niiname,'file')
@@ -50,7 +64,20 @@ function nii_tiff2nii (files)
     hdr.mat(3,4) = -0.5 * hdr.mat(3,3) * sz(3);
     hdr.dim = sz;
     hdr.pinfo = [0;0;0];
+    if maskborder ~= 0;
+        if maskborder == 1
+            msk = 0;
+        else
+            msk = 255;
+        end
+        img(img == img(2,2,1)) = msk;
+        img(:,end,:) = msk; %some JHU TIF images have wierd row
+    end
+    if invert
+       img = max(img(:)) - img; 
+    end
     spm_write_vol(hdr,img);
+
     nii_setOrigin12(hdr.fname,3,true);
 end;
 %end nii_tiff2nii()