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Remi-GauRemi-Gau
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refactor code for creation of ROIs from atlas
1 parent 1acf17d commit a53b52a

12 files changed

+123
-85
lines changed

‎atlas/visual_topography_probability_atlas.zip‎

32 Bytes
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‎demos/atlas/create_roi_from_atlas.m‎

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opt.roi.atlas = 'wang';
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opt.roi.name = {'V1v', 'V1d'};
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opt.roi.dir = fullfile(pwd, 'derivatives', 'cpp_roi', 'group');
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5+
spm_mkdir(opt.roi.dir);
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hemi = {'lh', 'rh'};
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9+
for iHemi = 1:numel(hemi)
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for iROI = 1:numel(opt.roi.name)
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roiName = opt.roi.name{iROI};
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imageName = extractRoiFromAtlas(opt.roi.dir, opt.roi.atlas, roiName, hemi{iHemi});
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end
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end

‎demos/roi/label_and_extract_clusters.m‎

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@@ -6,6 +6,8 @@
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% where each cluster has one label.
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%
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9+
run ../../initCppRoi;
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gunzip(fullfile('inputs', '*.gz'));
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zMap = fullfile(pwd, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');

‎demos/roi/other_demo.m‎

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% (C) Copyright 2021 CPP ROI developers
22

3+
run ../../initCppRoi;
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gunzip(fullfile('inputs', '*.gz'));
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zMap = fullfile(pwd, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
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‎demos/roi/roi_script.m‎

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clear;
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clc;
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run ../../initCppRoi;
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%% ASSUMPTION
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%
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% This assumes that the 2 immages are in the same space (MNI, individual)

‎src/atlas/extractRoiFromAtlas.m‎

Lines changed: 32 additions & 2 deletions
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@@ -1,7 +1,37 @@
11
% (C) Copyright 2021 CPP ROI developers
22

3-
function [imageName, imageVolume] = extractRoiFromAtlas(atlas, label, hemisphere)
3+
function roiImage = extractRoiFromAtlas(roiDir, atlas, roiName, hemisphere)
44

5-
[imageName, imageVolume] = extractRoiFromLabel(sourceImage, label, hemisphere);
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if strcmp(atlas, 'wang')
66

7+
[maxProbaFiles, roiLabels] = getRetinoProbaAtlas();
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if strcmp(hemisphere, 'lh')
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sourceImage = maxProbaFiles(1, :);
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else
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sourceImage = maxProbaFiles(2, :);
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end
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end
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roiIdx = strcmp(roiName, roiLabels.ROI);
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label = roiLabels.label(roiIdx);
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20+
labelStruct = struct('ROI', [hemisphere roiName], ...
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'label', label);
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roiImage = extractRoiByLabel(sourceImage, labelStruct);
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nameStructure = struct( ...
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'space', 'MNI', ...
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'hemi', hemisphere, ...
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'desc', atlas, ...
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'label', roiName, ...
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'type', 'mask', ...
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'ext', '.nii');
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newName = createFilename(nameStructure);
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movefile(roiImage, fullfile(roiDir, newName));
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roiImage = fullfile(roiDir, newName);
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end

‎src/atlas/getRetinoProbaAtlas.m‎

Lines changed: 4 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -15,54 +15,13 @@
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% PMID: 25452571
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% Probabilistic Maps of Visual Topography in Human Cortex
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%
18-
% If the data is not present in the ``cpp_spm/atlas/ProbAtlas_v4`` of the repo, it will be
19-
% downloaded and unzipped
2018

21-
README_URL = 'http://scholar.princeton.edu/sites/default/files/napl/files/readme.txt';
22-
ATLAS_URL = 'http://scholar.princeton.edu/sites/default/files/napl/files/probatlas_v4.zip';
19+
unzipAtlas('wang');
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24-
ATLAS_FOLDER = fullfile( ...
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fileparts(mfilename('fullpath')), ...
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'..', '..', 'atlas');
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atlasDir = returnAtlasDir('wang');
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28-
if ~exist(fullfile(ATLAS_FOLDER, 'ProbAtlas_v4'), 'dir')
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maxProbaFiles = spm_select('FPList', fullfile(atlasDir, 'subj_vol_all'), '^.*_dseg.nii$');
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30-
mkdir(ATLAS_FOLDER);
31-
32-
try
33-
urlwrite(ATLAS_URL, 'probatlas_v4.zip');
34-
unzip('probatlas_v4.zip', ATLAS_FOLDER);
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catch
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system(sprintf('curl -L %s -o probatlas_v4.zip', ATLAS_URL));
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unzip('probatlas_v4.zip', ATLAS_FOLDER);
38-
end
39-
40-
end
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42-
% urlwrite(README_URL, fullfile(ATLAS_FOLDER, 'ProbAtlas_v4', 'README.txt'));
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% urlread(README_URL)
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45-
maxProbaFiles = spm_select('FPListRec', ...
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fullfile(ATLAS_FOLDER, 'ProbAtlas_v4'), ...
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'^max.*.nii$');
48-
49-
if size(maxProbaFiles, 1) < 2
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51-
gunzip(fullfile(pwd, 'atlas', 'ProbAtlas_v4', 'subj_vol_all', 'max*.nii.gz'));
52-
53-
maxProbaFiles = spm_select('FPListRec', ...
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fullfile(ATLAS_FOLDER, 'ProbAtlas_v4'), ...
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'^max.*.nii$');
56-
57-
end
58-
59-
if size(maxProbaFiles, 1) < 2
60-
error('no atlas present');
61-
end
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63-
% the label file was created manually to be easier to load into SPM
64-
roiLabels = spm_load(spm_select('FPListRec', ...
65-
fullfile(ATLAS_FOLDER), ...
66-
'^ROI_labels_ProbAtlas_v4.csv$'));
25+
roiLabels = getRoiLabelLookUpTable('wang');
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end

‎src/atlas/getRoiLabelLookUpTable.m‎

Lines changed: 4 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -7,26 +7,19 @@
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return
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end
99

10+
atlasDir = returnAtlasDir(atlas);
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1012
switch lower(atlas)
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1214
case 'wang'
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14-
atlasDir = fullfile(fileparts(mfilename('fullpath')), ...
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'..', ...
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'..', ...
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'atlas');
18-
19-
roiLabelLUT = spm_load(fullfile(atlasDir, ...
20-
'visual_topography_probability_atlas', ...
21-
'LUT.csv'));
16+
roiLabelLUT = spm_load(fullfile(atlasDir, 'LUT.csv'));
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2318
case 'anatomy_toobox'
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2520
anat_tb_URL = 'https://www.fz-juelich.de/SharedDocs/Downloads/INM/INM-1/DE/Toolbox/Toolbox_22c.html';
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27-
spmDir = spm('dir');
28-
29-
roiLabelLUT = fullfile(spmDir, 'toolbox', 'Anatomy', 'Anatomy_v22c_MPM.txt');
22+
roiLabelLUT = fullfile(atlasDir, 'Anatomy_v22c_MPM.txt');
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3124
if ~exist(roiLabelLUT, 'file')
3225
error('Did you install the spm Anatomy toolbox?\n\nDownload it from: %s', ...

‎src/atlas/returnAtlasDir.m‎

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1+
% (C) Copyright 2021 CPP ROI developers
2+
3+
function atlasDir = returnAtlasDir(atlas)
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5+
atlasDir = fullfile(fileparts(mfilename('fullpath')), '..', '..', 'atlas');
6+
7+
if nargin > 0
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9+
switch atlas
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11+
case 'wang'
12+
atlasDir = fullfile(atlasDir, 'visual_topography_probability_atlas');
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14+
case 'anatomy_toobox'
15+
atlasDir = fullfile(spm('dir'), 'toolbox', 'Anatomy');
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17+
end
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19+
end
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21+
atlasDir = spm_file(atlasDir, 'cpath');
22+
23+
end

‎src/atlas/unzipAtlas.m‎

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@@ -1,19 +1,27 @@
11
% (C) Copyright 2021 CPP ROI developers
22

3-
function unzipAtlas()
3+
function unzipAtlas(atlas)
44

5-
atlasDir = fullfile(fileparts(mfilename('fullpath')), '..', '..', 'atlas');
5+
atlasDir = returnAtlasDir();
66

7-
file = fullfile(atlasDir, 'visual_topography_probability_atlas.zip');
7+
if strcmp(atlas, 'wang')
88

9-
unzip(file, fileparts(file));
9+
file = fullfile(atlasDir, 'visual_topography_probability_atlas.zip');
1010

11-
labelImages = spm_select('FPList', ...
12-
fullfile(atlasDir, ...
13-
'visual_topography_probability_atlas', ...
14-
'subj_vol_all'), ...
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'^maxprob_vol_.*h.nii.gz$');
11+
if ~exist(fullfile(atlasDir, 'visual_topography_probability_atlas'), 'dir')
1612

17-
gunzip(cellstr(labelImages));
13+
unzip(file, fileparts(file));
14+
15+
labelImages = spm_select('FPList', ...
16+
fullfile(atlasDir, ...
17+
'visual_topography_probability_atlas', ...
18+
'subj_vol_all'), ...
19+
'^.*_dseg.nii.gz$');
20+
21+
gunzip(cellstr(labelImages));
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23+
end
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25+
end
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1927
end

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