prepare binder and basic jupyter notebook

.gitignore

@@ -29,11 +29,13 @@ cfg/*
 group/*
 models/*
 
+# jupyter notebooks
+.ipynb_checkpoints
+
 ## MATLAB / OCTAVE gitignore template
 
 # From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
 
-
 # Windows default autosave extension
 *.asv
 

README.md

@@ -5,12 +5,10 @@
 [![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_SPM/workflows/CI/badge.svg)
 
 **Unit tests and coverage**
-
 [![codecov](https://codecov.io/gh/Remi-Gau/CPP_SPM/branch/master/graph/badge.svg?token=8IoRQtbFUV)](https://codecov.io/gh/Remi-Gau/CPP_SPM)
 
 **How to cite**

binder/apt.txt

@@ -0,0 +1,6 @@
+tree
+curl
+octave
+liboctave-dev
+gnuplot
+ghostscript

binder/environment.yml

@@ -0,0 +1,11 @@
+channels:
+
+- default
+- conda-forge
+
+dependencies:
+
+- octave_kernel
+- texinfo
+- jupyterlab
+- datalad=0.14

binder/postBuild

@@ -0,0 +1,16 @@
+mkdir ${HOME}/spm12 && curl -SL https://github.com/spm/spm12/archive/r7487.tar.gz | tar -xzC ${HOME}/spm12 --strip-components 1
+curl -SL https://raw.githubusercontent.com/spm/spm-docker/master/octave/spm12_r7487.patch | patch -d ${HOME}/spm12 -p3
+
+cd ${HOME}/spm12/src
+make PLATFORM=octave
+make PLATFORM=octave install
+
+cd ${HOME}/spm12/@file_array/private
+find . -name "mat2file*.*" -print0 | xargs -0 -I{} find '{}' \! -name "*.mex" -delete
+find . -name "file2mat*.*" -print0 | xargs -0 -I{} find '{}' \! -name "*.mex" -delete
+
+cd ${HOME}
+octave --no-gui --eval "addpath (fullfile (getenv (\"HOME\"), \"spm12\")); savepath ();"
+
+cd ${HOME}/demos/MoAE
+make inputs/raw

demos/MoAE/Makefile

@@ -15,12 +15,17 @@ clean:
 	rm -rf cfg
 	rm MoAEpilot.zip
 
-data:
-	datalad install git@gin.g-node.org:/RemiGau/spm_moae_fmriprep.git
-	datalad get spm_moae_fmriprep/*.json
-	datalad get spm_moae_fmriprep/sub*/*/*.nii.gz
-	datalad get spm_moae_fmriprep/sub*/*/*.tsv
-	datalad get spm_moae_fmriprep/sub*/*/*.json
+inputs/raw:
+	mkdir inputs/ -p
+	octave $(OCTFLAGS) --eval "run('download_moae_ds.m');exit;"
+
+inputs/fmriprep:
+	cd inputs && datalad install git@gin.g-node.org:/RemiGau/spm_moae_fmriprep.git
+	datalad get inputs/spm_moae_fmriprep/*.json
+	datalad get inputs/spm_moae_fmriprep/sub*/*/*.nii*
+	datalad get inputs/spm_moae_fmriprep/sub*/*/*.tsv
+	datalad get inputs/spm_moae_fmriprep/sub*/*/*.json
+	mv inputs/spm_moae_fmriprep inputs/fmriprep
 all: $(roi)
 
 $(preproc): moae_01_preproc.m

demos/MoAE/download_moae_ds.m

@@ -1,11 +1,15 @@
-function download_moae_ds(download_data)
+function download_moae_ds(download_data, clean)
   %
   % (C) Copyright 2021 Remi Gau
 
   if nargin < 1
     download_data = true;
   end
 
+  if nargin < 2
+    clean = false;
+  end
+
   if download_data
 
     % URL of the data set to download
@@ -14,7 +18,7 @@ function download_moae_ds(download_data)
     working_directory = fileparts(mfilename('fullpath'));
 
     % clean previous runs
-    if exist(fullfile(working_directory, 'inputs'), 'dir')
+    if clean && exist(fullfile(working_directory, 'inputs'), 'dir')
       rmdir(fullfile(working_directory, 'inputs'), 's');
     end
 

demos/MoAE/moae_01_preproc.m

@@ -7,18 +7,19 @@
 clc;
 
 download_data = false;
+clean = false;
 
 run ../../initCppSpm.m;
 
 opt = moae_get_option();
 
-download_moae_ds(download_data);
+% download_moae_ds(download_data, clean);
 
 % reportBIDS(opt);
 
 opt.pipeline.type = 'preproc';
 
-% bidsCopyInputFolder(opt);
+bidsCopyInputFolder(opt);
 
 % In case you just want to run segmentation and skull stripping
 % NOTE: skull stripping is also included in 'bidsSpatialPrepro'

demos/MoAE/moae_fmriprep_stats.m

@@ -1,8 +1,6 @@
 % This script will run the FFX and contrasts on it of the MoAE dataset
+% using the fmriprep preprocessed data
 %
-% Results might be a bit different from those in the manual as some
-% default options are slightly different in this pipeline
-% (e.g use of FAST instead of AR(1), motion regressors added)
 %
 % (C) Copyright 2019 Remi Gau
 

demos/MoAE/moae_get_option_fmriprep_preproc.m

@@ -19,6 +19,9 @@
 
   opt.space = {'MNI152NLin2009cAsym'};
 
+  opt.query.desc = {'preproc', 'confounds'};
+  %   opt.query.space = opt.space;
+
   %% DO NOT TOUCH
   opt = checkOptions(opt);
   saveOptions(opt);

demos/face_repetition/face_rep_01_preproc_func.m

@@ -8,7 +8,7 @@
 clear;
 clc;
 
-downloadData = true;
+downloadData = false;
 
 run ../../initCppSpm.m;
 

docker/Dockerfile

@@ -1,12 +1,11 @@
 # this is mostly taken from the spm docker files: https://github.com/spm/spm-docker
-FROM ubuntu:cosmic
+FROM ubuntu:focal
 
 # basic OS tools install and also octave
-RUN apt-get update && apt-get -y install --no-install-recommends \
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
      build-essential \
-     git \
-     zip unzip \
      curl \
+     git \
      octave \
      liboctave-dev \
  && apt-get clean \
@@ -16,7 +15,6 @@ RUN apt-get update && apt-get -y install --no-install-recommends \
      /var/lib/apt/lists/* \
      /var/log/apt/term*
 
-# install SPM and the relevant patches for octave
 RUN mkdir /opt/spm12 \
  && curl -SL https://github.com/spm/spm12/archive/r7487.tar.gz \
   | tar -xzC /opt/spm12 --strip-components 1 \
@@ -30,11 +28,10 @@ RUN mkdir /opt/spm12 \
 RUN octave --no-gui --eval "addpath(\"/opt/spm12\"); savepath ();"
 
 # get the CPP BIDS pipeline code
-RUN mkdir /CPP_BIDS_pipeline /output /code \
- && git clone https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline.git /CPP_BIDS_pipeline/
-
-RUN octave --no-gui --eval "addpath(genpath(\"/CPP_BIDS_pipeline\")); savepath ();"
+RUN mkdir /CPP_SPM /output /code \
+ && git clone https://github.com/cpp-lln-lab/CPP_SPM.git /CPP_SPM/
 
-WORKDIR /CPP_BIDS_pipeline
+RUN octave --no-gui --eval "addpath(genpath(\"/CPP_SPM/lib\")); savepath ();"
+RUN octave --no-gui --eval "addpath(genpath(\"/CPP_SPM/src\")); savepath ();"
 
-RUN git checkout remi-docker_dev
+WORKDIR /CPP_SPM

docs/source/docker.rst

@@ -1,26 +1,15 @@
 Docker
 ******
 
-The recipe to build the docker image is in the ``Dockerfile``
-
-Build docker image
-==================
-
-To build the image with with octave and SPM the `Dockerfile` just type::
-
-    docker build -t cpp_spm:0.0.1 .
-
-This will create an image with the tag name `cpp_spm_octave:0.0.1`
-
 Run docker image
 ================
 
-The following code would start the docker image and would map 2 folders one for
+The following code would pull and start the docker image and would map 2 folders one for
 ``output`` and one for ``code`` you want to run::
 
     docker run -it --rm \
     -v [output_folder]:/output \
-    -v [code_folder]:/code cpp_spm:0.0.1
+    -v [code_folder]:/code cpplab/cpp_spm:0.1.0
 
 To test it you can copy the ``MoAEpilot_run.m`` file in the ``demos/MoAE`` folder on
 your computer and then start running the docker and type::
@@ -32,3 +21,17 @@ your computer and then start running the docker and type::
 
     # To run the batch_download_run script
     octave --no-gui --eval MoAEpilot_run
+
+
+
+Build docker image locally
+==========================
+
+If you want to build the docker image locally and not pull it from the docker hub, the recipe to
+build the docker image is in the ``Dockerfile``
+
+To build the image with with octave and SPM the `Dockerfile` just type::
+
+    docker build -t cpp_spm:0.1.0 .
+
+This will create an image with the tag name `cpp_spm:0.1.0`