Merge pull request #404 from cpp-lln-lab/rc-1.1.0

[REL] rc 1.1.0

Author: Remi-Gau

.gitignore

@@ -1,39 +1,60 @@
-
+# General
 .DS_Store
-*.asv
-*.m~
-*.mat
+
 *.xml
 *.log
-*.html
 *.zip
+*.html
 *.ps
+*.png
 
+# Project specific
 options_task-*date*.json
 onsets*_events.mat
 
-# files in the demo folder related to running the demo analysis
-demos/*/outputs/
-demos/*/inputs/
-demos/*/*.nii
-demos/*/cfg/*.json
-
-# test folder and dummy data
-tests/*.png
-tests/group/*
-tests/*/*.json
-tests/dummyData/derivatives/cpp_spm*/sub-*/
-
-# ignore content of the build folder of the doc
-docs/build/*
-
-# ignore virtual env
+## virtual env
 cpp_spm/*
 env/*
+venv/*
 
-# visual studio code stuff
+## visual studio code
 .vscode
 
+## MATLAB / OCTAVE gitignore template
+
+# From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
+
+
+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Packaged app and toolbox files
+*.mlappinstall
+*.mltbx
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Simulink code generation folders
+slprj/
+sccprj/
+
+# Matlab code generation folders
+codegen/
+
+# Simulink autosave extension
+*.autosave
+
+# Simulink cache files
+*.slxc
 
+# Octave session info
+octave-workspace
 
 

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+repos:
+
+-   repo: local
+
+    hooks:
+
+    - id: mh_style
+      name: mh_style
+      entry: mh_style
+      args: [--process-slx, --fix]
+      files: ^(.*\.(m|slx))$
+      language: python
+      additional_dependencies: [miss_hit_core]
+
+    - id: mh_metric
+      name: mh_metric
+      entry: mh_metric
+      args: [--ci]
+      files: ^(.*\.(m|slx))$
+      language: python
+      additional_dependencies: [miss_hit_core]
+
+    - id: mh_lint
+      name: mh_lint
+      entry: mh_lint
+      files: ^(.*\.(m|slx))$
+      language: python
+      additional_dependencies: [miss_hit]

README.md

@@ -2,17 +2,15 @@
 
 **Documentation**
 
-[![Documentation Status: stable](https://readthedocs.org/projects/cpp-bids-spm/badge/?version=stable)](https://cpp-bids-spm.readthedocs.io/en/stable/?badge=stable)
+[![Documentation Status: stable](https://readthedocs.org/projects/cpp_spm/badge/?version=stable)](https://cpp_spm.readthedocs.io/en/stable/?badge=stable)
 
 **Code quality and style**
 
-[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/actions)
-![](https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/workflows/CI/badge.svg)
+[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_SPM/actions)
+![](https://github.com/cpp-lln-lab/CPP_SPM/workflows/CI/badge.svg)
 
 **Unit tests and coverage**
-
-[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline)
-[![codecov](https://codecov.io/gh/Remi-Gau/CPP_SPM/branch/master/graph/badge.svg?token=8IoRQtbFUV)](https://codecov.io/gh/Remi-Gau/CPP_SPM)
+[![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_SPM/branch/master/graph/badge.svg?token=8IoRQtbFUV)](https://codecov.io/gh/cpp-lln-lab/CPP_SPM)
 
 **How to cite**
 
@@ -62,7 +60,7 @@ initCppSpm
 ```
 
 Please see our
-[documentation](https://cpp-bids-spm.readthedocs.io/en/latest/index.html) for
+[documentation](https://cpp_spm.readthedocs.io/en/latest/index.html) for
 more detailed instructions.
 
 ### Dependencies
@@ -111,7 +109,7 @@ This can perform:
 The core functions are in the `src` folder.
 
 Please see our
-[documentation](https://cpp-bids-spm.readthedocs.io/en/latest/index.html) for
+[documentation](https://cpp_spm.readthedocs.io/en/latest/index.html) for
 more info.
 
 ## Octave compatibility
@@ -145,6 +143,23 @@ Scripts names in general and as well functions related to the demos use a
 
 Constant are written in `UPPERCASE`.
 
+#### Pre-commit
+
+There is a [pre-commit hook](https://pre-commit.com/) that you can use to
+reformat files as you commit them.
+
+Install pre-commit by using our `requirements.txt` file 
+```bash
+pip install -r requirements.txt
+```
+
+Install the hook
+```bash
+pre-commit install
+```
+
+You're done. `mh_style --fix` will now be run every time you commit.
+
 ## Contributors
 
 Thanks goes to these wonderful people

demos/.gitignore

@@ -0,0 +1,5 @@
+# files in the demo folder related to running the demo analysis
+*/outputs/
+*/inputs/
+*/*.nii
+*/cfg/*.json

demos/MoAE/moae_run.m

@@ -27,26 +27,29 @@
 bidsCopyRawFolder(opt, 1);
 
 % In case you just want to run segmentation and skull stripping
-% bidsSegmentSkullStrip(opt);
-%
 % NOTE: skull stripping is also included in 'bidsSpatialPrepro'
+bidsSegmentSkullStrip(opt);
 
 bidsSTC(opt);
 
 bidsSpatialPrepro(opt);
 
 % The following do not run on octave for now (because of spmup)
-anatomicalQA(opt);
-bidsResliceTpmToFunc(opt);
-functionalQA(opt);
-
+% anatomicalQA(opt);
+% bidsResliceTpmToFunc(opt);
+% functionalQA(opt);
+
+% create a whole brain functional mean image mask
+% so the mask will be in the same resolution/space as the functional images
+% one may not need it if they are running bidsFFX
+% since it creates a mask.nii by default
+opt.skullstrip.mean = 1;
+mask = bidsWholeBrainFuncMask(opt);
+
+% smoooth the funcitional images
 bidsSmoothing(FWHM, opt);
 
-% The following crash on CI
-WD = pwd;
+% The following crash on Travis CI
 bidsFFX('specifyAndEstimate', opt, FWHM);
-cd(WD);
 bidsFFX('contrasts', opt, FWHM);
-cd(WD);
 bidsResults(opt, FWHM);
-cd(WD);

demos/lesion_detection/batch_lesion.m

@@ -5,14 +5,15 @@
   %
   % USAGE::
   %
-  %  opt = Lesion_getOption()
+  %  opt = lesion_get_option()
   %
-  % :returns: - :optSource: (struct)
+  % :returns: - :opt: (struct)
   %
   % (C) Copyright 2021 CPP_SPM developers
 
   % The directory where the data are located
-  opt.dataDir = '/home/remi/gin/CVI-Datalad/data';
+  opt.dataDir = 'C:\Users\michm\Data\myphdproject\MRI\CVI-DataLad\data';
+  opt.derivativesDir = fullfile(opt.dataDir, '..', 'outputs');
 
   %% DO NOT TOUCH
   opt = checkOptions(opt);

demos/lesion_detection/lesion_get_option.m

@@ -0,0 +1,32 @@
+% (C) Copyright 2021 CPP_SPM developers
+
+clear;
+clc;
+
+% This script will will run
+% 1) lesion segmentation,
+% 2) lesion abnormalities detection and
+% 3) lesion overlapmap adapted from the ALI toolbox (SPM.)
+
+% URL of the data set to download
+% URL = https://gin.g-node.org/mwmaclean/CVI-Datalad/src/master/data
+
+run ../../initCppSpm.m;
+
+%% Set options
+opt = lesion_get_option();
+
+%% Run batches
+reportBIDS(opt);
+
+deleteZippedNii = true;
+bidsCopyRawFolder(opt, deleteZippedNii, {'anat'});
+
+% Step 1: segmentation
+bidsLesionSegmentation(opt);
+
+% % Step 2: lesion abnormalities
+bidsLesionAbnormalitiesDetection(opt);
+
+% % Step 3: overlap map
+% bidsLesionOverlapMap(opt)

demos/lesion_detection/run_lesion.m

@@ -6,10 +6,6 @@
   %
   % (C) Copyright 2020 CPP_SPM developers
 
-  if nargin < 1
-    opt = [];
-  end
-
   % The directory where the data are located
   opt.dataDir = '/home/remi/openneuro/ds000114/raw';
 
@@ -21,7 +17,6 @@
 
   opt.anatReference.type = 'T1w';
   opt.anatReference.session = 'retest';
-
   % Uncomment the lines below to run preprocessing
   % - don't use realign and unwarp
   %   opt.realign.useUnwarp = false;
@@ -30,11 +25,11 @@
 
   opt.model.file = fullfile(fileparts(mfilename('fullpath')), ...
                             'models', ...
-                            'model-ds000114-linebisection_smdl.json');
+                            'model-ds000114-lineBisectionRunLevel_smdl.json');
 
   % specify the result to compute
   opt.result.Steps(1) = struct( ...
-                               'Level',  'subject', ...
+                               'Level',  'run', ...
                                'Contrasts', struct( ...
                                                    'Name', 'Correct_Task', ... % has to match
                                                    'Mask', false, ...

demos/openneuro/ds000114_get_option.m

@@ -30,8 +30,31 @@
 
 bidsSmoothing(FWHM, opt);
 
+%% Run level analysis: as for MVPA
+
 bidsFFX('specifyAndEstimate', opt, FWHM);
 bidsFFX('contrasts', opt, FWHM);
+
+bidsConcatBetaTmaps(opt, FWHM, false, false);
+
+%% Subject level analysis: for regular univariate
+
+opt.model.file = fullfile(fileparts(mfilename('fullpath')), ...
+                          'models', ...
+                          'model-ds000114-linebisection_smdl.json');
+
+bidsFFX('specifyAndEstimate', opt, FWHM);
+
+opt.result.Steps(1) = struct( ...
+                             'Level',  'subject', ...
+                             'Contrasts', struct( ...
+                                                 'Name', 'Correct_Task', ... % has to match
+                                                 'Mask', false, ...
+                                                 'MC', 'FWE', ... FWE, none, FDR
+                                                 'p', 0.05, ...
+                                                 'k', 0));
+
+bidsFFX('contrasts', opt, FWHM);
 bidsResults(opt, FWHM);
 
 bidsRFX('smoothContrasts', opt, FWHM, conFWHM);