diff --git a/.travis.yml b/.travis.yml
index 87c8f835..31d8dde4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -39,7 +39,7 @@ before_script:
   # Add to src functions to path
   - octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath ();"
   # Change current directory
-  - cd manualTests
+  - cd tests/manualTests
 
 jobs:
   include:
diff --git a/manualTests/miss_hit.cfg b/manualTests/miss_hit.cfg
deleted file mode 100644
index d86aaeb0..00000000
--- a/manualTests/miss_hit.cfg
+++ /dev/null
@@ -1,9 +0,0 @@
-# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
-line_length: 100
-regex_function_name: "((test_[a-z]+)|[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
-
-# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
-metric "cnest": limit 4
-metric "file_length": limit 500
-metric "cyc": limit 15
-metric "parameters": limit 5
\ No newline at end of file
diff --git a/src/convertSourceToRaw.m b/src/convertSourceToRaw.m
index edb6dcaf..6a35504c 100644
--- a/src/convertSourceToRaw.m
+++ b/src/convertSourceToRaw.m
@@ -23,17 +23,13 @@ function convertSourceToRaw(cfg)
     rawDir = fullfile(cfg.dir.output, 'raw');
 
     % add dummy README and CHANGE file
-    copyfile(fullfile( ...
-                      fileparts(mfilename('fullpath')), '..', 'manualTests', 'dummyData', ...
-                      'README'), ...
+    templateFolder = fullfile(fileparts(mfilename('fullpath')), '..', 'templates');
+
+    copyfile(fullfile(templateFolder, 'README'), ...
              sourceDir);
-    copyfile(fullfile( ...
-                      fileparts(mfilename('fullpath')), '..', 'manualTests', 'dummyData', ...
-                      'CHANGES'), ...
+    copyfile(fullfile(templateFolder, 'CHANGES'), ...
              sourceDir);
-    copyfile(fullfile( ...
-                      fileparts(mfilename('fullpath')), '..', 'manualTests', 'dummyData', ...
-                      '.bidsignore'), ...
+    copyfile(fullfile(templateFolder, '.bidsignore'), ...
              sourceDir);
 
     copyfile(sourceDir, rawDir);
diff --git a/src/templates/test_templateTest.m b/src/templates/test_templateTest.m
index 73b91769..b293a352 100644
--- a/src/templates/test_templateTest.m
+++ b/src/templates/test_templateTest.m
@@ -23,6 +23,8 @@ function test_templateTestBasic()
     % expectedOuput = X;
 
     % assertEqual(actualOupout, expectedOuput)
+    % assertTrue( );
+    % assertFalse( );
 
     %% clean up (delete temporary files that were created)
 
diff --git a/manualTests/dummyData/.bidsignore b/templates/.bidsignore
similarity index 100%
rename from manualTests/dummyData/.bidsignore
rename to templates/.bidsignore
diff --git a/manualTests/dummyData/CHANGES b/templates/CHANGES
similarity index 100%
rename from manualTests/dummyData/CHANGES
rename to templates/CHANGES
diff --git a/manualTests/dummyData/README b/templates/README
similarity index 100%
rename from manualTests/dummyData/README
rename to templates/README
diff --git a/manualTests/dummyData/dummyData.nii.gz b/templates/dummyData.nii.gz
similarity index 100%
rename from manualTests/dummyData/dummyData.nii.gz
rename to templates/dummyData.nii.gz
diff --git a/tests/README.md b/tests/README.md
index 9d8452e4..c4ee1b18 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -6,23 +6,43 @@
 -   Install [MOcov for matlab and octave](https://github.com/MOcov/MOcov) to get
     the code coverage
 
--   Make sure you are in the `tests` directory.
+-   Make sure the following folders and sub-folders are in the Octave / MATLAB
+    path:
 
--   Run `moxunit_runtests` or `moxunit_runtests -verbose` to run the tests.
+    -   `src`
+    -   `lib`
+    -   `tests/utils`
+
+-   Run `moxunit_runtests tests` or `moxunit_runtests tests -verbose` to run the
+    tests.
 
 This should tell you which tests pass or fail.
 
-## code coverage
+## Adding more tests
+
+You can use the function template to write more tests.
+
+It is in the [`src/templates` folder](../src/templates)
+
+## Manual tests
+
+This is the folder where we keep tests that can not be run in continuous
+integration even as simple "smoke tests".
+
+<!-- ## code coverage
+
+A lot of what follows does not really work locally because of needing to add the right
+folders to the path to get an accurate coverage.
 
 The following command would give more info and will give you HTML output in a
 `coverage_html` folder showing you which lines of code is or is not checked by
 your test suite.
 
 ```matlab
-success = moxunit_runtests(pwd, ... % the path where the tests are
+success = moxunit_runtests('tests', ... % the path where the tests are
     '-verbose', ...
     '-with_coverage', ...
-    '-cover', fullfile(pwd, '..'), ... % the path of the code whose coverage we want to estimate
+    '-cover', fullfile(pwd, 'src'), ... % the path of the code whose coverage we want to estimate
     '-cover_xml_file','coverage.xml', ...
     '-cover_html_dir','coverage_html');
 ```
@@ -38,9 +58,9 @@ some tests.
 
 ```matlab
 coverage = mocov( ...
-    '-expression', 'moxunit_runtests()', ...
+    '-expression', "moxunit_runtests('test')", ...
     '-verbose', ...
-    '-cover', fullfile(pwd, '..'), ...
+    '-cover', fullfile(pwd, 'src'), ...
     '-cover_exclude', '*jsonread.m', ...
     '-cover_exclude', '*json*code.m', ...
     '-cover_exclude', '*Contents.m', ...
@@ -54,50 +74,4 @@ coverage = mocov( ...
     '-cover_exclude', '*test_*', ...
     '-cover_xml_file','coverage.xml', ...
     '-cover_html_dir','coverage_html')
-```
-
-## Adding more tests
-
-You can use the following function template to write more tests.
-
-```matlab
-function test_suite = test_functionToTest()
-    % This top function is necessary for mox unit to run tests.
-    % DO NOT CHANGE IT except to adapt the name of the function.
-    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
-        test_functions = localfunctions(); %#ok<*NASGU>
-    catch % no problem; early Matlab versions can use initTestSuite fine
-    end
-    initTestSuite;
-end
-
-function test_functionToTestBasic()
-
-    %% set up
-
-
-    %% data to test against
-
-
-    %% test
-    % assertTrue( );
-    % assertFalse( );
-    % assertEqual( );
-
-end
-
-function test_functionToTestUseCase1()
-
-    %% set up
-
-
-    %% data to test against
-
-
-    %% test
-    % assertTrue( );
-    % assertFalse( );
-    % assertEqual( );
-
-end
-```
+``` -->
diff --git a/manualTests/test_makeRawDataset.m b/tests/manualTests/test_makeRawDataset.m
similarity index 93%
rename from manualTests/test_makeRawDataset.m
rename to tests/manualTests/test_makeRawDataset.m
index 7008843f..c9a0d39d 100644
--- a/manualTests/test_makeRawDataset.m
+++ b/tests/manualTests/test_makeRawDataset.m
@@ -213,13 +213,15 @@ function test_makeRawDataset()
     createJson(cfg, extraInfo);
 
     %% add dummy data
+    templateFolder = fullfile(fileparts(mfilename('fullpath')), '..', '..', 'templates');
+
     subjectDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001');
     funcDir = fullfile(subjectDir, 'func');
 
     boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
 
     copyfile( ...
-             fullfile('dummyData', 'dummyData.nii.gz'), ...
+             fullfile(templateFolder, 'dummyData.nii.gz'), ...
              fullfile(funcDir, boldFilename));
 
     boldFilename = ['sub-001_ses-001_task-rest',  ...
@@ -227,7 +229,7 @@ function test_makeRawDataset()
                     '_run-001_echo-1_bold.nii.gz'];
 
     copyfile( ...
-             fullfile('dummyData', 'dummyData.nii.gz'), ...
+             fullfile(templateFolder, 'dummyData.nii.gz'), ...
              fullfile(funcDir, boldFilename));
 
     eegDir = fullfile(subjectDir, 'eeg');
@@ -241,19 +243,19 @@ function test_makeRawDataset()
     behFilename = 'sub-001_ses-001_task-easyTargetPractice_run-001_beh.tsv';
 
     copyfile( ...
-             fullfile('dummyData', 'dummyData.nii.gz'), ...
+             fullfile(templateFolder, 'dummyData.nii.gz'), ...
              fullfile(eegDir, eegFilename));
 
     copyfile( ...
-             fullfile('dummyData', 'dummyData.nii.gz'), ...
+             fullfile(templateFolder, 'dummyData.nii.gz'), ...
              fullfile(megDir, megFilename));
 
     copyfile( ...
-             fullfile('dummyData', 'dummyData.nii.gz'), ...
+             fullfile(templateFolder, 'dummyData.nii.gz'), ...
              fullfile(ieegDir, ieegFilename));
 
     copyfile( ...
-             fullfile('dummyData', 'dummyData.nii.gz'), ...
+             fullfile(templateFolder, 'dummyData.nii.gz'), ...
              fullfile(behDir, behFilename));
 
     %% actually do the conversion of the source data thus created
diff --git a/tests/dummyData/sub-blind01_ses-01_task-vislocalizer_events.tsv b/tests/testData/sub-blind01_ses-01_task-vislocalizer_events.tsv
similarity index 100%
rename from tests/dummyData/sub-blind01_ses-01_task-vislocalizer_events.tsv
rename to tests/testData/sub-blind01_ses-01_task-vislocalizer_events.tsv
diff --git a/tests/test_readAndFilterLogfile.m b/tests/test_readAndFilterLogfile.m
index cba936a7..b9f3275d 100644
--- a/tests/test_readAndFilterLogfile.m
+++ b/tests/test_readAndFilterLogfile.m
@@ -76,7 +76,7 @@ function test_readAndFilterLogfileFromFile()
 
     %% set up
 
-    inputFile = fullfile(fileparts(mfilename('fullpath')), 'dummyData', ...
+    inputFile = fullfile(fileparts(mfilename('fullpath')), 'testData', ...
                          'sub-blind01_ses-01_task-vislocalizer_events.tsv');
 
     % filter file