tanguyduval/spm12-apps

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

Install spm12 if you don't have it: https://www.fil.ion.ucl.ac.uk/spm/software/spm12/
[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

tanguyduval / spm12-apps