[FIX] fix demo vismotion

CHANGELOG.md

@@ -57,6 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+* [FIX] Fix vismotion demo (#1070) @Remi-Gau
 * [FIX] Exclude from GLM specification events with onsets longer than the run duration (#1060) @Remi-Gau
 * [FIX] remove dummies from preproc dataset and not raw dataset when using CLI (#1057) @Remi-Gau
 * [FIX] skip smoothing when running bidspm prepoc in dryRun (#1054) @Remi-Gau

demos/vismotion/README.md

@@ -34,7 +34,6 @@ all submodules.
 datalad install \
     -d . \
     -s https://github.com/cpp-lln-lab/bidspm.git \
-    --branch dev \
     -r \
     code/bidspm
 ```
@@ -44,7 +43,7 @@ initialize them manually, and update your dataset with that update
 
 ```bash
 cd code/bidspm
-git checkout dev
+git checkout main
 git submodule update --init --recursive && git submodule update --recursive
 cd ..
 datalad save -m 'update bidspm submodules'
@@ -65,6 +64,7 @@ This will install the data:
 datalad install -d . \
                 -s git@gin.g-node.org:/cpp-lln-lab/Trento_VisMotionLocalizer_MR_raw.git \
                 --recursive \
+                --jobs 12 \
                 inputs/raw
 ```
 

demos/vismotion/step_1_preprocess.m

@@ -3,15 +3,18 @@
 clear;
 clc;
 
-addpath(fullfile(pwd, '..', '..'));
+this_dir = fileparts(mfilename('fullpath'));
+bidspm_dir = fullfile(this_dir, '..', '..');
+addpath(bidspm_dir);
 bidspm();
 
-this_dir = fileparts(mfilename('fullpath'));
-root_dir = fullfile(this_dir, '..', '..', '..', '..');
+root_dir = fullfile(returnHomeDir(), 'visual_motion_localiser');
 
 bids_dir = fullfile(root_dir, 'inputs', 'raw');
 output_dir = fullfile(root_dir, 'outputs', 'derivatives');
 
+mkdir(output_dir);
+
 bidspm(bids_dir, output_dir, 'subject', ...
        'action', 'preprocess', ...
        'task', {'visMotion'}, ...

demos/vismotion/step_2_stats.m

@@ -3,26 +3,28 @@
 clear;
 clc;
 
-addpath(fullfile(pwd, '..', '..'));
+this_dir = fileparts(mfilename('fullpath'));
+bidspm_dir = fullfile(this_dir, '..', '..');
+addpath(bidspm_dir);
 bidspm();
 
-this_dir = fileparts(mfilename('fullpath'));
+root_dir = fullfile(returnHomeDir(), 'visual_motion_localiser');
+
 model_file = fullfile(this_dir, 'models', 'model-visMotionLoc_smdl.json');
-root_dir = fullfile(this_dir, '..', '..', '..', '..');
 bids_dir = fullfile(root_dir, 'inputs', 'raw');
 output_dir = fullfile(root_dir, 'outputs', 'derivatives');
 preproc_dir = fullfile(root_dir, 'outputs', 'derivatives', 'bidspm-preproc');
 
+%% subject level
+
 bidspm(bids_dir, output_dir, 'subject', ...
        'action', 'stats', ...
        'preproc_dir', preproc_dir, ...
-       'model_file', model_file, ...
-       'options', opt);
+       'model_file', model_file);
 
 %% dataset level
 
 bidspm(bids_dir, output_dir, 'dataset', ...
        'action', 'stats', ...
        'preproc_dir', preproc_dir, ...
-       'model_file', model_file, ...
-       'options', opt);
+       'model_file', model_file);

demos/vismotion/vismotion_demo.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 # fail whenever something is fishy, use -x to get verbose logfiles
-set -e -u
+set -e -u -x
 
 # IMPORTANT
 #
@@ -10,52 +10,73 @@ set -e -u
 #
 # What I used (see the line below) is very likely not where MATLAB lives on your computer
 #
-# /usr/local/MATLAB/R2017a/bin/matlab
+# /usr/local/MATLAB/R2018a/bin/matlab
 
-# create dataset in the home dir
-datalad create -c yoda ~/visual_motion_localiser
-cd ~/visual_motion_localiser
+yoda_dir=~/visual_motion_localiser
 
-# get bidspm code from the dev branch
-source="https://github.com/cpp-lln-lab/bidspm.git"
+# create a new dataset if it doesn't exist
+if [ ! -d ${yoda_dir} ]; then
 
-# for debugging uncomment the following lines
-# root_directory="${PWD}/../.."
-# source=${root_directory}
+    # create dataset in the home dir
+    datalad create -c yoda ${yoda_dir}
+    cd ${yoda_dir}
 
-datalad install \
-    -d . \
-    --source ${source} \
-    --branch dev \
-    --recursive \
-    code/bidspm
+    # get data
+    datalad install -d ${yoda_dir} \
+        --source git@gin.g-node.org:/cpp-lln-lab/Toronto_VisMotionLocalizer_MR_raw.git \
+        --get-data \
+        --jobs 12 \
+        inputs/raw
 
-# TODO: implement via bidspm bids app CLI only
-# cd code/bidspm
-# pip install .
-# cd ../..
+    datalad create -d ${yoda_dir} outputs/derivatives/bidspm-preproc
+    datalad create -d ${yoda_dir} outputs/derivatives/bidspm-stats
 
-# get data
-datalad install -d . \
-    --source git@gin.g-node.org:/cpp-lln-lab/Toronto_VisMotionLocalizer_MR_raw.git \
-    --get-data \
-    inputs/raw
+fi
 
-datalad create -d . outputs/derivatives/bidspm-preproc
-datalad create -d . outputs/derivatives/bidspm-stats
+# install bidspm if it doesn't exist
+if [ ! -d "${yoda_dir}/code/bidspm" ]; then
 
-cd code/bidspm/demos/vismotion
+    echo "installing bidspm in ${yoda_dir}/code/bidspm"
+
+    # get bidspm code
+    source="https://github.com/cpp-lln-lab/bidspm.git"
+
+    # for debugging uncomment the following lines
+
+    # # directory of this script
+    # script_directory="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+    # root_directory="${script_directory}/../.."
+    # # absolute path of root directory
+    # root_directory="$(readlink -f ${root_directory})"
+    # source=${root_directory}
+
+    echo "from ${source}"
+
+    datalad install \
+        -d ${yoda_dir} \
+        --source ${source} \
+        --recursive \
+        ${yoda_dir}/code/bidspm
+
+    # TODO: implement via bidspm bids app CLI only
+    # cd code/bidspm
+    # pip install .
+    # cd ../..
+
+fi
+
+cd ${yoda_dir}/code/bidspm/demos/vismotion
 
 # FIX ME
-/usr/local/MATLAB/R2017a/bin/matlab \
+/usr/local/MATLAB/R2018a/bin/matlab \
     -nodisplay -nosplash -nodesktop \
     -r "run('step_1_preprocess.m');exit;"
 
-datalad save -d ../../../.. -m 'preprocessing done' --recursive
+datalad save -d ${yoda_dir} -m 'preprocessing done' --recursive
 
 # FIX ME
-/usr/local/MATLAB/R2017a/bin/matlab \
+/usr/local/MATLAB/R2018a/bin/matlab \
     -nodisplay -nosplash -nodesktop \
     -r "run('step_2_stats.m');exit;"
 
-datalad save -d ../../../.. -m 'stats done' --recursive
+datalad save -d ${yoda_dir} -m 'stats done' --recursive

docs/source/conf.py

@@ -43,6 +43,8 @@
     "sphinxarg.ext",
 ]
 matlab_src_dir = os.path.dirname(os.path.abspath("../../src"))
+matlab_short_links = True
+matlab_auto_link = "basic"
 primary_domain = "mat"
 
 # Add any paths that contain templates here, relative to this directory.

src/IO/convertRealignParamToTsv.m

@@ -12,8 +12,7 @@
   %
   % :type  opt: structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
-  %             ``checkOptions()`` and ``loadAndCheckOptions()``.
+  %             See checkOptions.
   %
   % :type  rmInput: logical
   % :param rmInput: Optional. Default to ``false``.

src/IO/createDerivativeDir.m

@@ -8,7 +8,7 @@ function  createDerivativeDir(opt)
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
+  %             See checkOptions.
   %
 
   % (C) Copyright 2019 bidspm developers

src/IO/getData.m

@@ -8,7 +8,7 @@
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
+  %             See checkOptions.
   %
   % :param bidsDir: the directory where the data is ; default is :
   %                 ``fullfile(opt.dataDir, '..', 'derivatives', 'bidspm')``

src/IO/saveAndRunWorkflow.m

@@ -14,7 +14,7 @@
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
+  %             See checkOptions.
   % :type opt: structure
   %
   % :param subLabel: subject label

src/IO/saveOptions.m

@@ -8,7 +8,7 @@ function saveOptions(opt)
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
+  %             See checkOptions.
   %
 
   % (C) Copyright 2020 bidspm developers

src/QA/computeDesignEfficiency.m

@@ -26,7 +26,7 @@
   % :type tsvFile: char
   %
   % :param opt: Options chosen for the analysis.
-  %             See also: ``checkOptions()`` and ``loadAndCheckOptions()``.
+  %             See checkOptions.
   % :type  opt: structure
   %
   %

src/QA/mriqcQA.m

@@ -12,7 +12,7 @@ function mriqcQA(opt, suffix)
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
+  %             See checkOptions.
   %
   % EXAMPLE::
   %

src/QA/plotRoiTimeCourse.m

@@ -6,8 +6,7 @@
   %
   %   plotRoiTimeCourse(tsvFile, verbose, 'colors', colors, 'roiName', roiName)
   %
-  % :param tsvFile: obligatory argument.
-  %                 Content of TSV is organized in a "BIDS" way.
+  % :param tsvFile: Content of TSV is organized in a "BIDS" way.
   %                 Must be ``(t + 1) X c`` with t = time points and c = conditions.
   %                 The + 1 for the row dimension is because of the headers
   %                 giving the name of the condition.
@@ -25,7 +24,7 @@
   % :type roiName: char
   %
   %
-  % See also: bidsRoiBasedGLM(varargin)
+  % See also: bidsRoiBasedGLM
   %
 
   % (C) Copyright 2022 bidspm developers

src/QA/realignQA.m

@@ -1,10 +1,12 @@
 function [confoundsTsv, figureHandle] = realignQA(varargin)
   %
-  % implement different quality control fMRI realigned
+  % Implement different quality control fMRI realigned.
   %
-  % [confoundsTsv, figureHandle] = realignQA(boldFile, motionFile, ...
-  %                                          'radius', 50, ...
-  %                                          'visible', 'on')
+  % USAGE::
+  %
+  %   [confoundsTsv, figureHandle] = realignQA(boldFile, motionFile, ...
+  %                                            'radius', 50, ...
+  %                                            'visible', 'on')
   %
   %
   % Adapted from Cyril Pernet's spmup

src/batches/preproc/setBatchCoregistration.m

@@ -11,7 +11,7 @@
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
+  %             See checkOptions.
   %
   % :param ref: Reference image
   % :type ref: char

src/batches/preproc/setBatchCoregistrationFmap.m

@@ -11,7 +11,7 @@
   %              See also: bids.layout, getData.
   %
   % :param opt: Options chosen for the analysis.
-  %             See also: ``checkOptions()`` and ``loadAndCheckOptions()``.
+  %             See checkOptions.
   % :type  opt: structure
   %
   % :param subLabel:

src/batches/preproc/setBatchCoregistrationFuncToAnat.m

@@ -15,7 +15,7 @@
   %              See also: bids.layout, getData
   %
   % :param opt: Options chosen for the analysis.
-  %             See also: ``checkOptions()`` and ``loadAndCheckOptions()``.
+  %             See checkOptions.
   % :type  opt: structure
   %
   % :param subLabel: subject label

src/batches/preproc/setBatchCreateVDMs.m

@@ -14,7 +14,7 @@
   %              See also: bids.layout, getData.
   %
   % :param opt: Options chosen for the analysis.
-  %             See also: ``checkOptions()`` and ``loadAndCheckOptions()``.
+  %             See checkOptions.
   % :type  opt: structure
   %
   % :param subLabel: subject label

src/batches/preproc/setBatchGenerateT1map.m

@@ -14,7 +14,7 @@
   % :type BIDS: structure
   %
   % :param opt: Options chosen for the analysis.
-  %             See also: ``checkOptions()`` and ``loadAndCheckOptions()``.
+  %             See checkOptions.
   % :type  opt: structure
   %
   % :param subLabel: subject label

src/batches/preproc/setBatchNormalizationSpatialPrepro.m

@@ -11,7 +11,7 @@
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
+  %             See checkOptions.
   %
   % :param voxDim:
   % :type opt: array

src/batches/preproc/setBatchRealign.m

@@ -18,7 +18,7 @@
   %              See also: bids.layout, getData.
   %
   % :param opt: Options chosen for the analysis.
-  %             See also: ``checkOptions()`` and ``loadAndCheckOptions()``.
+  %             See checkOptions.
   % :type  opt: structure
   %
   % :param subLabel: subject label

src/batches/preproc/setBatchRenameSegmentParameter.m

@@ -10,7 +10,7 @@
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
+  %             See checkOptions.
   %
   %
   % :returns: - :matlabbatch: (cell) The matlabbatch ready to run the spm job

src/batches/preproc/setBatchReslice.m

@@ -11,7 +11,7 @@
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
-  %             See also: checkOptions
+  %             See checkOptions.
   %
   % :param referenceImg: Reference image (only one image)
   % :type  referenceImg: char or cellstring