Merge pull request #84 from cpp-lln-lab/fix_gunzip

[FIX] gunzipping with octave

Author: Remi-Gau

src/atlas/extractRoiFromAtlas.m

@@ -8,7 +8,7 @@
   %   roiImage = extractRoiFromAtlas(outputDir, atlasName, roiName, hemisphere)
   %
   % :param outputDir:
-  % :param atlasName: ``wang``, ``neuromorphometrics``, ``'hcpex'``
+  % :param atlasName: ``'wang'``, ``'visfatlas'``, ``'neuromorphometrics'``, ``'hcpex'``
   % :param roiName: run ``getLookUpTable(atlasName)`` to get a list of ROI names to choose from
   % :param hemisphere: ``L`` or ``R``
   % :type outputDir: string

src/atlas/unzipAtlas.m

@@ -21,15 +21,23 @@ function unzipAtlas(atlas)
                                            'subj_vol_all'), ...
                                   '^.*_dseg.nii.gz$');
 
-        gunzip(cellstr(labelImages));
+        if isOctave()
+          gunzipWithOctave(cellstr(labelImages));
+        else
+          gunzip(cellstr(labelImages));
+        end
 
       end
 
     case 'visfatlas'
 
       file = fullfile(atlasDir, 'visfAtlas/space-MNI_atlas-visfAtlas_dseg.nii.gz');
 
-      gunzip(file);
+      if isOctave()
+        gunzipWithOctave(file);
+      else
+        gunzip(file);
+      end
 
     case 'hcpex'
 
@@ -39,11 +47,17 @@ function unzipAtlas(atlas)
 
       file = fullfile(returnAtlasDir('hcpex'), 'HCPex.nii.gz');
       if isOctave()
-        copyfile(file, fullfile(returnAtlasDir('hcpex'), 'HCPex.nii.gz.bak'));
+        gunzipWithOctave(file);
+      else
+        gunzip(file);
       end
 
-      gunzip(file);
-
   end
 
 end
+
+function gunzipWithOctave(file)
+  copyfile(file, [file '.bak']);
+  gunzip(file);
+  copyfile([file '.bak'], file);
+end