Merge pull request #80 from cpp-lln-lab/add_new_atlas

Remi-Gau · web-flow · commit 53a12b5c8746 · 2022-12-14T17:16:16.000+01:00
[ENH] add HPC extended atlas
diff --git a/.gitmodules b/.gitmodules
@@ -2,3 +2,6 @@
 	path = lib/marsbar
 	url = https://github.com/marsbar-toolbox/marsbar.git
 	datalad-url = https://github.com/marsbar-toolbox/marsbar.git
+[submodule "atlas/HCPex"]
+	path = atlas/HCPex
+	url = https://github.com/wayalan/HCPex.git
diff --git a/README.md b/README.md
@@ -66,7 +66,10 @@ as a submodule, and initialized when running `initCppSpm`.
     -   neurosynth probability maps
     -   the probabilistic maps of visual topography in human cortex [@wang2014]
         -   https://scholar.princeton.edu/napl/resources
-    -   the probabilistic functional atlas of human occipito-temporal visual cortex [@rosenke2020]
+    -   the probabilistic functional atlas of human occipito-temporal visual
+        cortex [@rosenke2020]
+    -   [extended Human Connectome Project multimodal parcellation atlas](https://github.com/wayalan/HCPex.git)
+        of the human cortex and subcortical areas [@huang_extended_2022]
 
 Also includes:
 
diff --git a/atlas/HCPex b/atlas/HCPex
@@ -0,0 +1 @@
+Subproject commit 543e88b9ac9a5e05d3a6c82d941de696e42baa9a
diff --git a/atlas/HCPex.xml b/atlas/HCPex.xml
diff --git a/atlas/miss_hit.cfg b/atlas/miss_hit.cfg
@@ -0,0 +1 @@
+exclude_dir: "HCPex"
diff --git a/atlas/returnAtlasDir.m b/atlas/returnAtlasDir.m
@@ -25,6 +25,9 @@
       case 'visfatlas'
         atlasDir = fullfile(atlasDir, 'visfAtlas');
 
+      case 'hcpex'
+        atlasDir = fullfile(atlasDir, 'HCPex', 'HCPex_v1.0');
+
       case 'neuromorphometrics'
 
       otherwise
diff --git a/initCppRoi.m b/initCppRoi.m
@@ -28,6 +28,10 @@ function initCppRoi()
     catch
     end
 
+    unzipAtlas('hcpex');
+    copyAtlasToSpmDir('HCPex', 'verbose', true);
+    copyAtlasToSpmDir('AAL', 'verbose', true);
+
     CPP_ROI_INITIALIZED = true();
 
   else
diff --git a/references.bib b/references.bib
@@ -27,3 +27,19 @@ @article{wang2014
   url     = {https://doi.org/10.1093/cercor/bhu277},
   eprint  = {https://academic.oup.com/cercor/article-pdf/25/10/3911/14102011/bhu277.pdf}
 }
+
+@article{huang_extended_2022,
+	title = {An extended {Human} {Connectome} {Project} multimodal parcellation atlas of the human cortex and subcortical areas},
+	volume = {227},
+	issn = {1863-2653, 1863-2661},
+	url = {https://link.springer.com/10.1007/s00429-021-02421-6},
+	doi = {10.1007/s00429-021-02421-6},
+	language = {en},
+	number = {3},
+	urldate = {2022-12-14},
+	journal = {Brain Structure and Function},
+	author = {Huang, Chu-Chung and Rolls, Edmund T. and Feng, Jianfeng and Lin, Ching-Po},
+	month = apr,
+	year = {2022},
+	pages = {763--778},
+}
diff --git a/src/atlas/copyAtlasToSpmDir.m b/src/atlas/copyAtlasToSpmDir.m
@@ -27,13 +27,17 @@ function copyAtlasToSpmDir(varargin)
   verbose = args.Results.verbose;
 
   spmAtlasDir = fullfile(spm('dir'), 'atlas');
-  cppRoiAtlasDir = returnAtlasDir();
 
   switch lower(atlas)
 
     case 'aal'
-      sourceAtlasImage = fullfile(cppRoiAtlasDir, 'AAL3', 'AAL3v1_1mm.nii.gz');
-      sourceAtlasXml = fullfile(cppRoiAtlasDir, 'AAL3', 'AAL3v1_1mm.xml');
+      sourceAtlasImage = fullfile(returnAtlasDir(), 'AAL3', 'AAL3v1_1mm.nii.gz');
+      sourceAtlasXml = fullfile(returnAtlasDir(), 'AAL3', 'AAL3v1_1mm.xml');
+
+    case 'hcpex'
+      sourceAtlasImage = fullfile(returnAtlasDir('hcpex'), 'HCPex.nii.gz');
+      sourceAtlasXml = fullfile(returnAtlasDir(), 'HCPex.xml');
+
   end
 
   targetAtlasImage = fullfile(spmAtlasDir, spm_file(sourceAtlasImage, 'filename'));
diff --git a/src/atlas/extractRoiFromAtlas.m b/src/atlas/extractRoiFromAtlas.m
@@ -8,7 +8,7 @@
   %   roiImage = extractRoiFromAtlas(outputDir, atlasName, roiName, hemisphere)
   %
   % :param outputDir:
-  % :param atlasName: ``wang``, ``neuromorphometrics``
+  % :param atlasName: ``wang``, ``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
@@ -61,6 +61,10 @@
 
     roiIdx = strcmp([prefix roiName], lut.ROI);
 
+  elseif strcmpi(atlasName, 'hcpex')
+
+    roiIdx = strcmp([hemisphere '_' roiName], lut.ROI);
+
   end
 
   % create ROI
diff --git a/src/atlas/getAtlasFilename.m b/src/atlas/getAtlasFilename.m
@@ -2,27 +2,17 @@
   %
   % Returns the atlas filename
   %
-  % "Probabilistic Maps of Visual Topography in Human Cortex"
-  %
   % USAGE::
   %
   %   atlasFilename = getAtlasFilename(atlasName)
   %
   %
-  %   DOI 10.1093/cercor/bhu277
-  %   PMCID: PMC4585523
-  %   PMID: 25452571
-  %   Probabilistic Maps of Visual Topography in Human Cortex
-  %
 
   % (C) Copyright 2021 CPP ROI developers
 
   atlasDir = returnAtlasDir(atlasName);
 
-  if ~ismember(lower(atlasName), {'wang', 'neuromorphometrics', 'anatomy_toobox', 'visfatlas'})
-    % TODO throw a proper error here
-    error('unknown atlas type');
-  end
+  isAKnownAtlas(atlasName);
 
   switch lower(atlasName)
 
@@ -51,6 +41,10 @@
 
       atlasFilename = fullfile(atlasDir, 'space-MNI_atlas-visfAtlas_dseg.nii');
 
+    case 'hcpex'
+
+      atlasFilename = fullfile(atlasDir, 'HCPex.nii');
+
   end
 
 end
diff --git a/src/atlas/getLookUpTable.m b/src/atlas/getLookUpTable.m
@@ -20,10 +20,7 @@
 
   atlasDir = returnAtlasDir(atlasName);
 
-  if ~ismember(lower(atlasName), {'wang', 'neuromorphometrics', 'anatomy_toobox', 'visfatlas'})
-    % TODO throw a proper error here
-    error('unknown atlas type');
-  end
+  isAKnownAtlas(atlasName);
 
   switch lower(atlasName)
 
@@ -56,6 +53,22 @@
       roiLabelLUT = struct('ROI', C(1), ...
                            'label', C(2));
 
+    case 'hcpex'
+
+      roiLabelLUT = fullfile(atlasDir, 'HCPex.nii.txt');
+
+      fid = fopen(roiLabelLUT);
+      pattern = '%f%s%s%f';
+      C = textscan(fid, pattern, 'Headerlines', 1);
+      fclose(fid);
+
+      for i = 1:numel(C{2})
+        ROI{1}{i} = [C{2}{i} '_' C{3}{i}];
+      end
+
+      roiLabelLUT = struct('ROI', ROI(1), ...
+                           'label', C(1));
+
     case 'visfatlas'
 
       unzipAtlas('visfAtlas');
diff --git a/src/atlas/isAKnownAtlas.m b/src/atlas/isAKnownAtlas.m
@@ -0,0 +1,11 @@
+function isAKnownAtlas(atlasName)
+  % (C) Copyright 2021 CPP ROI developers
+  if ~ismember(lower(atlasName), {'wang', ...
+                                  'neuromorphometrics', ...
+                                  'anatomy_toobox', ...
+                                  'visfatlas', ...
+                                  'hcpex'})
+    % TODO throw a proper error here
+    error('unknown atlas type');
+  end
+end
diff --git a/src/atlas/unzipAtlas.m b/src/atlas/unzipAtlas.m
@@ -5,29 +5,44 @@ function unzipAtlas(atlas)
 
   atlasDir = returnAtlasDir();
 
-  if strcmp(atlas, 'wang')
+  switch lower(atlas)
 
-    file = fullfile(atlasDir, 'visual_topography_probability_atlas.zip');
+    case 'wang'
 
-    if ~exist(fullfile(atlasDir, 'visual_topography_probability_atlas'), 'dir')
+      file = fullfile(atlasDir, 'visual_topography_probability_atlas.zip');
 
-      unzip(file, fileparts(file));
+      if ~exist(fullfile(atlasDir, 'visual_topography_probability_atlas'), 'dir')
 
-      labelImages =  spm_select('FPList', ...
-                                fullfile(atlasDir, ...
-                                         'visual_topography_probability_atlas', ...
-                                         'subj_vol_all'), ...
-                                '^.*_dseg.nii.gz$');
+        unzip(file, fileparts(file));
 
-      gunzip(cellstr(labelImages));
+        labelImages =  spm_select('FPList', ...
+                                  fullfile(atlasDir, ...
+                                           'visual_topography_probability_atlas', ...
+                                           'subj_vol_all'), ...
+                                  '^.*_dseg.nii.gz$');
 
-    end
+        gunzip(cellstr(labelImages));
 
-  elseif strcmp(atlas, 'visfAtlas')
+      end
 
-    file = fullfile(atlasDir, 'visfAtlas/space-MNI_atlas-visfAtlas_dseg.nii.gz');
+    case 'visfatlas'
 
-    gunzip(file);
+      file = fullfile(atlasDir, 'visfAtlas/space-MNI_atlas-visfAtlas_dseg.nii.gz');
+
+      gunzip(file);
+
+    case 'hcpex'
+
+      if exist(fullfile(returnAtlasDir('hcpex'), 'HCPex.nii'), 'file')
+        return
+      end
+
+      file = fullfile(returnAtlasDir('hcpex'), 'HCPex.nii.gz');
+      if isOctave()
+        copyfile(file, fullfile(returnAtlasDir('hcpex'), 'HCPex.nii.gz.bak'));
+      end
+
+      gunzip(file);
 
   end
 
diff --git a/src/utils/isOctave.m b/src/utils/isOctave.m
@@ -0,0 +1,21 @@
+function retval = isOctave()
+  %
+  % Returns true if the environment is Octave.
+  %
+  % USAGE::
+  %
+  %   retval = isOctave()
+  %
+  % :returns: :retval: (boolean)
+  %
+
+  % (C) Copyright 2022 CPP ROI developers
+
+  persistent cacheval   % speeds up repeated calls
+
+  if isempty (cacheval)
+    cacheval = (exist ('OCTAVE_VERSION', 'builtin') > 0);
+  end
+
+  retval = cacheval;
+end
diff --git a/tests/test_copyAtlasToSpmDir.m b/tests/test_copyAtlasToSpmDir.m
@@ -24,3 +24,21 @@ function test_copyAtlasToSpmDir_basic()
   assertEqual(exist(targetAtlasXml, 'file'), 2);
 
 end
+
+function test_copyAtlasToSpmDir_HPCex()
+
+  if isGithubCi()
+    return
+  end
+
+  copyAtlasToSpmDir('HCPex', 'verbose', false);
+
+  spmAtlasDir = fullfile(spm('dir'), 'atlas');
+
+  targetAtlasImage = fullfile(spmAtlasDir, 'HCPex.nii');
+  targetAtlasXml = fullfile(spmAtlasDir, 'HCPex.xml');
+
+  assertEqual(exist(targetAtlasImage, 'file'), 2);
+  assertEqual(exist(targetAtlasXml, 'file'), 2);
+
+end
diff --git a/tests/test_extractRoiFromAtlas.m b/tests/test_extractRoiFromAtlas.m
@@ -56,3 +56,21 @@ function test_extractRoiFromAtlas_visfAtlas()
   delete(fullfile(pwd, '*.json'));
 
 end
+
+function test_extractRoiFromAtlas_hcpex()
+
+  unzipAtlas('hcpex');
+
+  roiImage = extractRoiFromAtlas(pwd, 'hcpex', 'MT', 'L');
+
+  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_atlas-hcpex_label-MT_mask.nii'), ...
+                    'file'), ...
+              2);
+
+  vol =  spm_read_vols(spm_vol(roiImage));
+  assertEqual(sum(vol(:) == 1), 620); % check the ROI has the right number of voxel
+
+  delete(fullfile(pwd, '*.nii'));
+  delete(fullfile(pwd, '*.json'));
+
+end
diff --git a/tests/test_getAtlasFilename.m b/tests/test_getAtlasFilename.m
@@ -13,9 +13,11 @@ function test_getAtlasFilename_wang()
   rmRetinoAtlas();
 
   atlasFilename = getAtlasFilename('wang');
-
   assertEqual(size(atlasFilename, 1), 2);
 
+  atlasFilename = getAtlasFilename('HCPex');
+  assertEqual(size(atlasFilename, 1), 1);
+
   rmRetinoAtlas();
 
 end
diff --git a/tests/test_getLookUpTable.m b/tests/test_getLookUpTable.m
@@ -34,6 +34,15 @@ function test_lut_anat_tb()
 
 end
 
+function test_lut_hcpex()
+
+  lut = getLookUpTable('hcpex');
+
+  assertEqual(lut.label, [2:426]');
+  assertEqual(lut.ROI{417}, 'R_Gpe');
+
+end
+
 function test_lut_neuromorpho()
 
   lut = getLookUpTable('neuromorphometrics');
diff --git a/tests/test_unzipAtlas.m b/tests/test_unzipAtlas.m
@@ -21,6 +21,13 @@ function test_unzipAtlas_default()
                     'file'), ...
               2);
 
+  unzipAtlas('hcpex');
+
+  assertEqual(exist( ...
+                    fullfile(returnAtlasDir('hcpex'), 'HCPex.nii'), ...
+                    'file'), ...
+              2);
+
   cleanUp();
 
 end
