feat: adapt sample scripts for parallel testing

juancarlosfarah · Oct 8, 2021 · f5f5f75 · f5f5f75
1 parent bf33a5e
commit f5f5f75
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Showing 8 changed files with 25 additions and 22 deletions.
diff --git a/src/matlab/builders/configurations/BuildBrainExtractionConfiguration.m b/src/matlab/builders/configurations/BuildBrainExtractionConfiguration.m
@@ -14,7 +14,7 @@
 % get data folder relative to this file
 filePath = fileparts(which(mfilename));
 pathToDataFolder = fullfile(filePath, '../../../../../neurochi/data/');
-pathToWorkspace = fullfile(pathToDataFolder, 'w1');
+pathToWorkspace = fullfile(pathToDataFolder, 'workspace');
 pathToDataset = fullfile(pathToDataFolder, 'input');
 % for intermediary pipelines, send output to the transfer folder
 pathToOutput = fullfile(pathToDataFolder, 'transfer');
@@ -27,8 +27,8 @@
 config.pathToDataset = pathToDataset;
 config.pathToOutput = pathToOutput;
 % helps debug by not running all subjects
-config.numSubjects = 1;
-config.parallel = false;
+config.numSubjects = 2;
+config.parallel = true;
 
 % sequence level configurations
 config.sequence.startStep = 1;

diff --git a/src/matlab/builders/configurations/BuildFunctionalConnectivityConfiguration.m b/src/matlab/builders/configurations/BuildFunctionalConnectivityConfiguration.m
@@ -13,7 +13,7 @@
 % get data folder relative to this file
 filePath = fileparts(which(mfilename));
 pathToDataFolder = fullfile(filePath, '../../../../../neurochi/data/');
-pathToWorkspace = fullfile(pathToDataFolder, 'w1');
+pathToWorkspace = fullfile(pathToDataFolder, 'workspace');
 pathToDataset = fullfile(pathToDataFolder, 'input');
 % for intermediary pipelines, send output to the transfer folder
 pathToOutput = fullfile(pathToDataFolder, 'transfer');
@@ -26,8 +26,8 @@
 config.pathToDataset = pathToDataset;
 config.pathToOutput = pathToOutput;
 % helps debug by not running all subjects
-config.numSubjects = 1;
-config.parallel = false;
+config.numSubjects = 2;
+config.parallel = true;
 config.numPcaComponents = 5;
 
 % sequence level configurations

diff --git a/src/matlab/builders/configurations/BuildRegisterToStandardConfiguration.m b/src/matlab/builders/configurations/BuildRegisterToStandardConfiguration.m
@@ -13,7 +13,7 @@
 % get data folder relative to this file
 filePath = fileparts(which(mfilename));
 pathToDataFolder = fullfile(filePath, '../../../../../neurochi/data/');
-pathToWorkspace = fullfile(pathToDataFolder, 'w1');
+pathToWorkspace = fullfile(pathToDataFolder, 'workspace');
 pathToDataset = fullfile(pathToDataFolder, 'input');
 pathToParcellations = fullfile(pathToDataFolder, 'parcs');
 % for intermediary pipelines, send output to the transfer folder
@@ -28,8 +28,8 @@
 config.pathToParcellations = pathToParcellations;
 config.pathToOutput = pathToOutput;
 % helps debug by not running all subjects
-config.numSubjects = 1;
-config.parallel = false;
+config.numSubjects = 2;
+config.parallel = true;
 
 % sequence level configurations
 config.sequence.startStep = 1;

diff --git a/src/matlab/builders/configurations/BuildSegmentationConfiguration.m b/src/matlab/builders/configurations/BuildSegmentationConfiguration.m
@@ -1,4 +1,4 @@
-function [config] = BuildSegmentationConfiguration()
+function [config] = BuildSegmentationConfiguration(parcellation)
 %BUILDSEGMENTATIONCONFIGURATION Builds configuration for a pipeline.
 %   Builds a configuration for a pipeline that performs segmentation.
 %
@@ -13,7 +13,7 @@
 % get data folder relative to this file
 filePath = fileparts(which(mfilename));
 pathToDataFolder = fullfile(filePath, '../../../../../neurochi/data/');
-pathToWorkspace = fullfile(pathToDataFolder, 'w1');
+pathToWorkspace = fullfile(pathToDataFolder, 'workspace');
 pathToDataset = fullfile(pathToDataFolder, 'input');
 pathToParcellations = fullfile(pathToDataFolder, 'parcs');
 % for intermediary pipelines, send output to the transfer folder
@@ -28,9 +28,9 @@
 config.pathToParcellations = pathToParcellations;
 config.pathToOutput = pathToOutput;
 % helps debug by not running all subjects
-config.numSubjects = 1;
-config.parcellation = 'schaefer_2018_400_subc';
-config.parallel = false;
+config.numSubjects = 2;
+config.parcellation = parcellation;
+config.parallel = true;
 
 % sequence level configurations
 config.sequence.startStep = 1;

diff --git a/src/matlab/builders/configurations/BuildTransformParcellationConfiguration.m b/src/matlab/builders/configurations/BuildTransformParcellationConfiguration.m
@@ -1,4 +1,4 @@
-function [config] = BuildTransformParcellationConfiguration()
+function [config] = BuildTransformParcellationConfiguration(parcellation)
 %BUILDTRANSFORMPARCELLATIONCONFIGURATION Builds configuration for pipeline.
 %   Builds a configuration for a pipeline that transforms a parcellation.
 %
@@ -13,7 +13,7 @@
 % get data folder relative to this file
 filePath = fileparts(which(mfilename));
 pathToDataFolder = fullfile(filePath, '../../../../../neurochi/data/');
-pathToWorkspace = fullfile(pathToDataFolder, 'w1');
+pathToWorkspace = fullfile(pathToDataFolder, 'workspace');
 pathToDataset = fullfile(pathToDataFolder, 'input');
 pathToParcellations = fullfile(pathToDataFolder, 'parcs');
 % for intermediary pipelines, send output to the transfer folder
@@ -28,15 +28,15 @@
 config.pathToParcellations = pathToParcellations;
 config.pathToOutput = pathToOutput;
 % helps debug by not running all subjects
-config.numSubjects = 1;
+config.numSubjects = 2;
 % select the parcellation to transform
 % (must be present in `pathToParcellations`)
 % usually you use first a parcellation
 % e.g. 'schaefer_2018_400_subc.nii'
 % and then a ventricle atlas
 % e.g. 'mask_ventricles_MNIch2.nii.gz'
-config.parcellation = 'schaefer_2018_400_subc.nii';
-config.parallel = false;
+config.parcellation = parcellation;
+config.parallel = true;
 
 % sequence level configurations
 config.sequence.startStep = 1;

diff --git a/src/matlab/scripts/registerParcellationScript.m b/src/matlab/scripts/registerParcellationScript.m
@@ -2,7 +2,8 @@
 clearvars;
 
 % build configuration
-config = BuildSampleConfiguration();
+parcellation = 'shen_MNI152';
+config = BuildSampleConfiguration(parcellation);
 
 pipeline = BuildRegisterParcellationPipeline(config.common.pathToWorkspace, ...
                                              config.common.pathToDataset, ...

diff --git a/src/matlab/scripts/segmentationScript.m b/src/matlab/scripts/segmentationScript.m
@@ -6,7 +6,8 @@
 addpath(genpath(fullfile(filePath, '../../matlab')));
 
 % build configuration
-config = BuildSegmentationConfiguration();
+parcellation = 'shen_MNI152';
+config = BuildSegmentationConfiguration(parcellation);
 
 pipeline = BuildSegmentationPipeline(config.parcellation, ...
                                      config.pathToWorkspace, ...

diff --git a/src/matlab/scripts/transformParcellationScript.m b/src/matlab/scripts/transformParcellationScript.m
@@ -6,7 +6,8 @@
 addpath(genpath(fullfile(filePath, '../../matlab')));
 
 % build configuration
-config = BuildTransformParcellationConfiguration();
+parcellation = 'shen_MNI152';
+config = BuildTransformParcellationConfiguration(parcellation);
 
 pipeline = BuildTransformParcellationPipeline(config.parcellation, ...
                                               config.pathToWorkspace, ...