tanguyduval/spm12-apps

New neuroimaging technologies in SPM: BIDS, docker, boutique, and quality control

This repository includes the following spm apps:

• BIDS: for dicom to BIDS conversion and for parsing a BIDS folder. BIDS is the standard for neuroimaging data organization: http://bids.neuroimaging.io
• Boutiques: for running any dockerized neuroimaging tool (e.g. FSL, Freesurfer, ANTs, ...). Boutiques is the standard describing these tools https://boutiques.github.io/
• Quality Control: includes a module for exporting nifti results as an interactive Html page and an advanced Nifti viewer with ROI tools (for drawing a mask).

Documentation

• ISMRM Abstract
• Installation
• Features
  • BIDS parser module: create a participant BIDS pipeline in just a minute
  • Boutiques (run FSL, ANTS, Freesurfer, ... or any command)

INSTALL

1. Install spm12 if you don't have it: https://www.fil.ion.ucl.ac.uk/spm/software/spm12/
2. [R2014b or later] Copy-Paste in your Matlab command line:

% CHANGE DIRECTORY to default Matlab path
if isempty(userpath), userpath('reset'); end
cd(userpath)
% DOWNLOAD spm-apps
websave('spm12-apps.zip','https://github.com/tanguyduval/spm12-apps/archive/master.zip')
unzip spm12-apps.zip
% ADD to Matlab path
addpath(fullfile('spm12-apps-master','BIDS'))
addpath(fullfile('spm12-apps-master','Boutiques'))
addpath(fullfile('spm12-apps-master','QualityControl'))
savepath
% RUN spm Batch Editor
cfg_util('initcfg')
cfg_ui

[R2014a or older] In spm Batch Editor: File-->Add Application-->select cfg_mlbatch_appcfg.m in each folder

FEATURES

BIDS parser module

create a participant BIDS pipeline in just a minute

• download an example BIDS dataset: https://openneuro.org/datasets/ds001378/versions/00003
• open the matlabbatch using command cfg_ui
• Add a new module Parse BIDS

• Fill module as follows

• Preview your BIDS dataset

• add a new module BasicIO>FileOperation>Gunzip files
• Use the dependency button and select one modality (e.g. dwi) and fill as follows

• Add additional modules or just click the run icon. Subject 1 session 1 will be processed.
  Results will be saved into bidsfolder/derivatives/matlabbatch/sub-NAME/ses-SESSION/DWI/
• Click on the run for all subjects icon (double play icon) to loop across all subjects/sessions
• Save your single participant pipeline using the save icon into a m-file
• Share your pipeline.

Boutiques

(run FSL, ANTS, Freesurfer, ... or your own app)

• install and run docker (https://www.docker.com/get-started). highly recommanded. Note: On windows 8 and older, install docker toolbox: https://docs.docker.com/toolbox/toolbox_install_windows/

Use pre-existing Boutiques files

• Download a 4D image https://openneuro.org/crn/datasets/ds001378/snapshots/00003/files/sub-control01:ses-01:dwi:sub-control01_ses-01_dwi.nii.gz
• open the Batch Editor using command cfg_ui
• Use a fslmaths>Tmean module to average across time:

Create a Custom Boutiques file

• Add a new Generic module

  • Fill the module as follows
    Use Docker: docker images with preinstalled neuroimaging softwares can be found on https://hub.docker.com/
    bids/mrtrix3-connectome includes ANTS MRtrix3 and FSL docker images will be automatically downloaded and inputs/output folders mounted
    if you choose "NO", command will be run locally
  
  • RUN the command using the green play button
  • Save your preset module as a Boutiques descriptor https://boutiques.github.io
    
    
  
  • Reload modules

cfg_util('initcfg')
cfg_ui

• Use your preset module in an other pipeline

• Your preset is saved under spm-apps\Boutiques\Boutiques