Merge pull request #38 from marcobarilari/marco_add-visfAtlas

Add visfAtlas

Author: marcobarilari

Makefile

@@ -3,6 +3,10 @@
 clean:
 	rm -rf coverage*
 	rm version.txt
+
+clean_lib:
+	rm -rf lib/bids-matlab
+
 install_dev:
 	git clone https://github.com/bids-standard/bids-matlab.git --branch dev --depth 1 lib/bids-matlab
 

README.md

@@ -70,6 +70,11 @@ as a submodule, and intitialized when running `initCppSpm`.
             Probabilistic Maps of Visual Topography in Human Cortex. Cerebral
             cortex (New York, N.Y. : 1991), 25(10), 3911–3931.
             https://doi.org/10.1093/cercor/bhu277
+    -   the probabilistic functional atlas of human occipito-temporal visual cortex
+        -   Rosenke, M., van Hoof, R., van den Hurk, J., Grill-Spector, K., & Goebel, R. (2021).
+            A Probabilistic Functional Atlas of Human Occipito-Temporal Visual Cortex.
+            Cerebral cortex (New York, N.Y. : 1991), 31(1), 603–619.
+            https://doi.org/10.1093/cercor/bhaa246
 
 Also includes:
 

atlas/returnAtlasDir.m

@@ -14,14 +14,21 @@
 
   if nargin > 0
 
-    switch atlas
+    switch lower(atlas)
 
       case 'wang'
         atlasDir = fullfile(atlasDir, 'visual_topography_probability_atlas');
 
       case 'anatomy_toobox'
         atlasDir = fullfile(spm('dir'), 'toolbox', 'Anatomy');
 
+      case 'visfatlas'
+        atlasDir = fullfile(atlasDir, 'visfAtlas');
+
+      case 'neuromorphometrics'
+
+      otherwise
+        error('unknown atlas type');
     end
 
   end

atlas/visfAtlas/LUT.csv

@@ -0,0 +1,34 @@
+label,ROI,func
+1,lh_mFus,faces
+2,lh_pFus,faces
+3,lh_IOG,faces
+4,lh_OTS,bodies
+5,lh_ITG,bodies
+6,lh_MTG,bodies
+7,lh_LOS,bodies
+8,lh_pOTS,characters
+9,lh_IOS,haracters
+10,lh_CoS,places
+11,lh_hMT,motion
+12,lh_v1d,retinotopic
+13,lh_v2d,retinotopic
+14,lh_v3d,retinotopic
+15,lh_v1v,retinotopic
+16,lh_v2v,retinotopic
+17,lh_v3v,retinotopic
+18,rh_mFus,faces
+19,rh_pFus,faces
+20,rh_IOG,faces
+21,rh_OTS,bodies
+22,rh_ITG,bodies
+23,rh_MTG,bodies
+24,rh_LOS,bodies
+25,rh_CoS,places
+26,rh_TOS,places
+27,rh_hMT,motion
+28,rh_v1d,retinotopic
+29,rh_v2d,retinotopic
+30,rh_v3d,retinotopic
+31,rh_v1v,retinotopic
+32,rh_v2v,retinotopic
+33,rh_v3v,retinotopic

atlas/visfAtlas/README.md

@@ -0,0 +1,16 @@
+visfAtlas in nifti volume format
+
+The visfAtlas is based on N19 subjects. In FreeSurfer, it is aligned to the fsaverage brain. In BrainVoyager, it is aligned to a newly generated average brain for BrainVoyager, called the BVaverage. The BVaverage is distributed with this publication. The nifti volume atlas is aligned to the MNI colin27 brain.
+
+Citing:
+
+Please cite the article for use of the functional atlas as well as the BVaverage.
+
+Rosenke, M., van Hoof, R., van den Hurk, J., Goebel, R. (2020). A probabilistic functional parcellation of human occipito-temporal cortex. TBD
+
+To acknowledge using this atlas in your research, you might include a sentence like one of the following:
+
+"We used the functional atlas of visual cortex developed by Rosenke et al. (2020)…”
+
+
+The maximum probability map can be visualized by opening the visfATlas\_volume.nii.gz file and loading the correct color map (visfAtlas\_FSL.cmap) through the overlay display panel.

atlas/visfAtlas/space-MNI_atlas-visfAtlas_dseg.nii.gz

@@ -1,12 +1,18 @@
 % (C) Copyright 2021 CPP ROI developers
 
-opt.roi.atlas = 'wang';
-opt.roi.name = {'V1v', 'V1d'};
+clear all;
+clc;
+
+% options : 'wang', 'neuromorphometrics', 'anatomy_toobox', 'visfAtlas'
+opt.roi.atlas = 'visfAtlas';
+
+% to get the list of possible run `getLookUpTable(opt.roi.atlas)`
+opt.roi.name = {'pFus', 'mFus', 'CoS'};
 opt.roi.dir = fullfile(pwd, 'derivatives', 'cpp_roi', 'group');
 
 spm_mkdir(opt.roi.dir);
 
-hemi = {'L', 'H'};
+hemi = {'L', 'R'};
 
 for iHemi = 1:numel(hemi)
 

demos/atlas/create_roi_from_atlas.m

@@ -18,19 +18,25 @@
   %
   % (C) Copyright 2021 CPP ROI developers
 
+  if ~ismember(hemisphere, {'L', 'R'})
+
+    error('\n Hemisphere label %s not valid, try "L" or "R"', hemisphere);
+
+  end
+
   [atlasFile, lut] = getAtlasAndLut(atlasName);
 
-  if strcmp(atlasName, 'wang')
+  if strcmpi(atlasName, 'wang')
 
-    if strcmp(hemisphere, 'L')
+    if strcmpi(hemisphere, 'L')
       atlasFile = atlasFile(1, :);
     else
       atlasFile = atlasFile(2, :);
     end
 
     roiIdx = strcmp(roiName, lut.ROI);
 
-  elseif strcmp(atlasName, 'neuromorphometrics')
+  elseif strcmpi(atlasName, 'neuromorphometrics')
 
     roiName = regexprep(roiName, '(Left )|(Right )', '');
 
@@ -43,6 +49,17 @@
 
     roiIdx = strcmp([prefix roiName], lut.ROI);
 
+  elseif strcmpi(atlasName, 'visfatlas')
+
+    prefix = '';
+    if strcmp(hemisphere, 'L')
+      prefix = 'lh_';
+    elseif strcmp(hemisphere, 'R')
+      prefix = 'rh_';
+    end
+
+    roiIdx = strcmp([prefix roiName], lut.ROI);
+
   end
 
   % create ROI

src/atlas/extractRoiFromAtlas.m

@@ -18,7 +18,7 @@
 
   atlasDir = returnAtlasDir(atlasName);
 
-  if ~ismember(atlasName, {'wang', 'neuromorphometrics', 'anatomy_toobox'})
+  if ~ismember(lower(atlasName), {'wang', 'neuromorphometrics', 'anatomy_toobox', 'visfatlas'})
     % TODO throw a proper error here
     error('unknown atlas type');
   end
@@ -46,6 +46,10 @@
 
       error('not implemented yet');
 
+    case 'visfatlas'
+
+      atlasFilename = fullfile(atlasDir, 'space-MNI_atlas-visfAtlas_dseg.nii');
+
   end
 
 end

src/atlas/getAtlasFilename.m

@@ -19,7 +19,7 @@
 
   atlasDir = returnAtlasDir(atlasName);
 
-  if ~ismember(atlasName, {'wang', 'neuromorphometrics', 'anatomy_toobox'})
+  if ~ismember(lower(atlasName), {'wang', 'neuromorphometrics', 'anatomy_toobox', 'visfatlas'})
     % TODO throw a proper error here
     error('unknown atlas type');
   end
@@ -55,6 +55,12 @@
       roiLabelLUT = struct('ROI', C(1), ...
                            'label', C(2));
 
+    case 'visfatlas'
+
+      unzipAtlas('visfAtlas');
+
+      roiLabelLUT = spm_load(fullfile(atlasDir, 'LUT.csv'));
+
   end
 
 end

src/atlas/getLookUpTable.m

@@ -22,6 +22,12 @@ function unzipAtlas(atlas)
 
     end
 
+  elseif strcmp(atlas, 'visfAtlas')
+
+    file = fullfile(atlasDir, 'visfAtlas/space-MNI_atlas-visfAtlas_dseg.nii.gz');
+
+    gunzip(file);
+
   end
 
 end

src/atlas/unzipAtlas.m

@@ -49,7 +49,7 @@ function test_createRoi_intersection_mask_sphere()
 
   mask = createRoi('intersection', specification, volumeDefiningImage, outputDir, saveImg);
 
-  basename = 'rspace-MNI_atlas-neurosynth_label-visualMotionIntersection_desc-p10pt00_mask';
+  basename = 'space-MNI_atlas-neurosynth_label-visualMotionIntersection_desc-p10pt00_mask';
 
   assertEqual(exist(fullfile(thisDir(), [basename '.nii']), 'file'), 2);
   assertEqual(exist(fullfile(thisDir(), [basename '.json']), 'file'), 2);
@@ -75,7 +75,7 @@ function test_createRoi_intersection_mask_sphere()
 
   mask = createRoi('expand', specification, volumeDefiningImage, outputDir, saveImg);
 
-  basename = 'rspace-MNI_atlas-neurosynth_label-visualMotionExpandVox57_desc-p10pt00_mask';
+  basename = 'space-MNI_atlas-neurosynth_label-visualMotionExpandVox57_desc-p10pt00_mask';
 
   assertEqual(mask.roi.size, 57);
 
@@ -95,7 +95,8 @@ function test_createRoi_intersection_mask_sphere()
 
   value = fullfile(thisDir(), '..', 'demos', 'roi', 'inputs');
 
-  if exist(fullfile(value, 'TStatistic.nii'), 'file') == 0
+  if exist(fullfile(value, 'TStatistic.nii'), 'file') == 0 || ...
+     exist(fullfile(value, 'visual motion_association-test_z_FDR_0.01.nii'), 'file') == 0
     gunzip(fullfile(value, '*.gz'));
   end
 
@@ -106,7 +107,7 @@ function test_createRoi_intersection_mask_sphere()
   volumeDefiningImage = fullfile(demoDir(), 'TStatistic.nii');
 
   roiFilename = fullfile(demoDir(), ...
-                         'rspace-MNI_atlas-neurosynth_label-visualMotion_desc-p10pt00_mask.nii');
+                         'space-MNI_atlas-neurosynth_label-visualMotion_desc-p10pt00_mask.nii');
 
   if exist(roiFilename, 'file') == 2
 
@@ -117,6 +118,8 @@ function test_createRoi_intersection_mask_sphere()
     zMap = renameNeuroSynth(zMap);
     zMap = resliceRoiImages(volumeDefiningImage, zMap);
 
+    zMap = removePrefix(zMap, 'r');
+
     threshold = 10;
     roiFilename = thresholdToMask(zMap, threshold);
 

tests/test_createRoi.m

@@ -28,14 +28,9 @@ function test_createRoiName_non_sphere()
   roiName = createRoiName(mask);
   assertEqual(roiName, 'one-entity_mask.nii');
 
-  % This will likely break when bids-matlab is updated and the order of entities
-  % is imposed by the schema
-  %
-  % label-foo_one-entity_mask.nii
-  %
   mask.label = 'foo';
   roiName = createRoiName(mask);
-  assertEqual(roiName, 'one-entity_label-foo_mask.nii');
+  assertEqual(roiName, 'label-foo_one-entity_mask.nii');
 
 end
 

tests/test_createRoiName.m

@@ -40,3 +40,19 @@ function test_extractRoiFromAtlas_neuromorphometrics()
   delete(fullfile(pwd, '*.json'));
 
 end
+
+function test_extractRoiFromAtlas_visfAtlas()
+
+  roiImage = extractRoiFromAtlas(pwd, 'visfatlas', 'pFus', 'L');
+
+  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_atlas-visfatlas_label-pFus_mask.nii'), ...
+                    'file'), ...
+              2);
+
+  vol =  spm_read_vols(spm_vol(roiImage));
+  assertEqual(sum(vol(:) == 1), 655); % check the ROI has the right number of voxel
+
+  delete(fullfile(pwd, '*.nii'));
+  delete(fullfile(pwd, '*.json'));
+
+end

tests/test_extractRoiFromAtlas.m

@@ -43,6 +43,15 @@ function test_lut_neuromorpho()
 
 end
 
+function test_lut_visfAtlas()
+
+  lut = getLookUpTable('visfatlas');
+
+  assertEqual(lut.label, [1:33]');
+  assertEqual(lut.ROI{1}, 'lh_mFus');
+
+end
+
 function cleanUp()
 
   pause(1);

tests/test_getLookUpTable.m

@@ -10,7 +10,7 @@
 
 function test_returnAtlasDir_default()
 
-  atlasDir = returnAtlasDir('neuromorphometric');
+  atlasDir = returnAtlasDir('neuromorphometrics');
 
   assertEqual(atlasDir, returnAtlasDir());