ABCD docker (Ver: 251)

Overview

The Multi-Modal Processing Stream (MMPS) is a software package that consists of binaries, scripts, and matlab functions, designed collectively to process data from non-invasive brain imaging methods. These modalities include structural MRI (sMRI; T1w, T2w), diffusion tensor imaging (dMRI; DTI, restriction spectrum imaging), resting-state functional MRI (rs-fMRI), and task-based fMRI (task-fMRI), representing a range of temporal and spatial resolutions, physiological and anatomical sensitivities, and fields of view. The challenge therein is to combine simultaneous and complementary information from different imaging techniques in order to provide comprehensive analyses across a variety of research applications; the MMPS provides a simple yet powerful interface to do just this, and has aided the understanding of normal function in sleep, memory and language, development and aging, and diseases such as dementia, epilepsy, and autism. The tools in this package were written by several members of the University of California, San Diego Multimodal Imaging Laboratory (MMIL) now the Center for Multimodal Imaging and Genetics (CMIG), including: Don Hagler, Anders Dale, Vijay Venkatraman, Dominic Holland, Nate White, Cooper Roddey, Alain Koyama, Jason Sherfey, Rajan Patel, Ben Cippolini, Hauke Bartsch, Feng Xue, Octavio Ruiz De Leon, Sean Hatton, and M. Daniela Cornejo. The MMPS docker image is a portable version of the MMPS pipeline. This pipeline has scripts, binaries and compiled matlab scripts that are needed for MRI data processing. The ABCD shared tabulated data and miniproc data are generated by using this pipeline. Packages shipped with this pipeline:

FSL, Ver:5.0.2.2-centos6_64
Freesurfer, Ver: 530
AFNI, Ver: 2010_10_19_1028
MMPS, Ver: 251
Dcm2niix, Ver: trunk
dtitk, Ver: 2.3.1-Linux-x86_64
gosu, Ver: 1.11
Matlab Compiler Runtime, Ver: v84
dcmtk, Ver: 3.6.0
Some scripts from SPM5b

Prerequisites

• Host OS. This docker container has been tested under Centos 7.4.1708. It has not been tested under Microsoft Windows.
• Memory and storage for docker
  • At least 6GB memory is required to run all processing steps, 12GB is recommended.
  • On Mac, 64GB disk image size is recommended (the uncompressed MMPS docker is approximately 22GB).
• FreeSurfer license. A personal FreeSurfer license needs to be obtained from https://surfer.nmr.mgh.harvard.edu/registration.html. Please note, version of FreeSurfer is 530.

Recommendations

Use ABCD protocol, simple classify bval/bvecs from header in Philips/Seimens, from file for GE

Installation

1. download these three necessary files:

   • abcd dockerfile and script (Dockerfile and abcddocker_installer.sh)
   • mmps_home.tar.gz
   • run_abcd_docker.sh

2. build docker image:

build -t abcd .

This may take at least half an hour depends on your network bandwidth. 3. In a temporary location, unpack the mmps_home.tar.gz file that contains the necessary scripts and data that will be mounted to the docker container’s /home/MMPS directory:

• .cshrc: shell enviorment configuration file that defines the version of several necessary software packages.
• bin/: binary folder contains necessary scripts, which are explained in run_abcd_docker.sh
• ProjInfo/MMIL_ProjInfo.csv: This is the project setup configuration file. There is an example setup for project: DAL_ABCD. This file defines location of necessary processing directories and some necessary parameters.
• ProjInfo/$ProjID/${ProjID}_*_ProcSteps.csv: these are processing steps files that defines parameters needed for each processing step. Each step is explained in run_abcd_docker.sh
• ProjInfo/network_*: containers parcellation maps

4. To configure a project, modify the run_abcd_docker.sh script. Please input appropriate values for these following variables:
   • ProjID: (your project id, example: DAL_ABCD)
   • FSLic: (where you saved the obtained FreeSurfer license from step 1. example: pwd/.license
   • HomeRoot: location that the mmps_home.tar.gz is extracted to from step 1, such as the host download directory. Example: /Users/dsmith/Download/mmps_home
   • RawDataRoot: location where the fast-track tgz files are, this has to be a path inside the docker container. Example: /home/MMPS/data/fast-track
   • You may also adjust the processing step configuration files as required.

Processing steps

Please also check notes inside $HomeRoot/bin/run_preparedata.sh:

1. Data preparation: The $HomeRoot/bin/run_preparedata.sh will create the necessary directories, unpack the compressed tgz files and move them into appropriate locations.
2. Initial data summary: The $HomeRoot/bin/run_incoming_report.sh will summarize all unpacked imaging series based on those json files. It will also save the summary to /home/MMPS/MetaData/$ProjID/${ProjID}_incoming_info.csv This step is optional but recommended
3. Preprocessing: In this step, DICOM data will first be converted into mgz format, then different correction processes will run for different modality (e.g. dMRI files will be corrected for motion/bias field/B0/Eddy current etc.) This will run preprocessing steps based on: infix_list in $HomeRoot/bin/run_ABCD_pre.sh and the proc step files for each preprocessing step. For example, there are four preprocessing steps in run_ABCD_pre.sh now, which are: pc, proc, fsurf, and proc_dMRI. Their associated proc step file are:

/home/MMPS/ProjInfo/$ProjID/${ProjID}_pc_ProcSteps.csv
/home/MMPS/ProjInfo/$ProjID/${ProjID}_proc_ProcSteps.csv
/home/MMPS/ProjInfo/$ProjID/${ProjID}_freesurfer_ProcSteps.csv
/home/MMPS/ProjInfo/$ProjID/${ProjID}_proc_dMRI_ProcSteps.csv

Those proc step files contains necessary parameters for processing. You may change them for your own need but default is recommended. Here are some description for those preprocessing steps:

• pc: protocol compliance check, this is necessary for fMRI analysis
• proc: DICOM to mgz conversion and corrections (motion/bias field/eddy current etc.)
• freesurfer: freesurfer surface reconstruction
• proc_dMRI: specific DTI data processing

4. Protocol compliance check summary: The run_summarizePC.sh will summarize result of the pc step and save the summary to /home/MMPS/MetaData/$ProjID/${ProjID}_pcinfo.csv. This step has to be run after pc. This summary will be used by the fMRI data analysis
5. Postprocessing: This will run postprocessing steps based on: infix_list in /home/MMPS/bin/run_ABCD_post.sh and the proc step files for each step. For example, there are 16 postprocessing steps in run_ABCD_post.sh now, which are:

analysis steps:

analyze_sMRI
analyze_dMRI
analyze_DTI_full
analyze_behav
analyze_rsBOLD
analyze_taskBOLD

summary steps:

summarize_DTI
summarize_DTI_full
summarize_RSI
summarize_MRI
summarize_MRI_info
summarize_rsBOLD_aparc2_networks
summarize_rsBOLD_aparc2_subcort
summarize_rsBOLD_aparc2_var
summarize_taskBOLD
summarize_behav

They also have associated proc step file in /home/MMPS/ProjInfo/$ProjID/. Those proc step files contains necessary parameters for processing. You may change them for your own need but default is recommended. If succeeded, you may find summarized results in /home/MMPS/MetaData/$ProjID/ROI_Summaries

Creating your own project

You may also follow steps below to create your own project(s): Let’s say, you want to create a new project called ABCD_NEW (case sensitive). And you did the following:

1. unpacked mmps_home.tar.gz to /path/to/mmps_home
2. Put fast-track tgzs under /path/to/mmps_home/data/fast-track
3. Put freesurfer license under /path/to/freesurfer/.license Now, let’s first create a record in MMPS_ProjInfo.csv as below:
4. Create a new line, put ABCD_NEW for the ProjID column
5. Change name for the PI column unless you are at DAIC.
6. Change path value for columns below. Please remember, the paths are inside docker container not on the host. If you want to specify paths out of /home/MMPS, you will need to mount it in the docker container using -v option first. Here we suppose that you want to put all processing folders under /home/MMPS/data/ABCD_NEW. Below, please find lists of column names of the ProjInfo file on the left side and values accordingly on the right side.

incoming → /home/MMPS/data/ABCD_NEW/incoming
unpack → /home/MMPS/data/ABCD_NEW/unpack
pc → /home/MMPS/data/ABCD_NEW/pc
qc → /home/MMPS/data/ABCD_NEW/qc
orig → /home/MMPS/data/ABCD_NEW/orig
raw → /home/MMPS/data/ABCD_NEW/raw
proc → /home/MMPS/data/ABCD_NEW/proc
proc_dti → /home/MMPS/data/ABCD_NEW/proc_dti
proc_bold → /home/MMPS/data/ABCD_NEW/proc_bold
fsurf → /home/MMPS/data/ABCD_NEW/fsurf
fsico → /home/MMPS/data/ABCD_NEW/fsico

Please do not change values for other columns unless you know the meaning. After that, let’s create a ProjInfo folder for project ABCD_NEW using command below:

cp -a /path/to/mmps_home/ProjInfo/DAL_ABCD /path/to/mmps_home/ProjInfo/ABCD_NEW

Then rename those DAL_ABCD_* files to ABCD_NEW_*, for example:

mv /path/to/mmps_home/ProjInfo/ABCD_NEW/DAL_ABCD_Series_Classify.csv /path/to/mmps_home/ProjInfo/ABCD_NEW/ABCD_NEW_Series_Classify.csv

Next, you may change parameter inside those proc step files for your own need. Thus, we finished making project info record and proc step files. Now, let’s modify parameters in the run_abcd_docker.sh as below:

• ProjID=ABCD_NEW
• FSLic=/path/to/freesurfer/.license
• HomeRoot=/path/to/mmps_home
• RawDataRoot=/home/MMPS/data/fast-track You may also change processing steps inside the run_abcd_docker.sh script for your own need. You may even make your own script and put it in /path/to/mmps_home/bin and change -c parameter of docker to execute it. Finally, let’s execute the run_abcd_docker.sh script and sit back. It may run for hours (or even longer) depending on the processing steps you choose and the size of the dataset. Don’t forget to put on your power adapter if you are running on laptop.