Run Code with Docker

Docker is a boon to research and get's past the issue of "runs on my machine" by making a portable, entirely reproducible environment.

This guide will set you up to run the code via docker.

1. download docker on your machine 2a. (coming soon) via the commandline, type docker pull hbclab/restingstate. 2b. If the above doesn't work (I haven't set it up yet). you need to:

• clone the repository: git clone https://github.com/HBClab/RestingState.git
• build the docker image (while in the same directory as the Dockerfile: docker build -t hbclab/restingstate .

3. Run the image.

Example

I have a bid(ish) organized dataset like so

ds005
├── CHANGES
├── dataset_description.json
├── derivatives
│   ├── bet
│   │   └── sub-01
│   │       └── anat
│   │           └── sub-01_desc-brainmask_T1w.nii.gz
│   └── data
│       └── roi_list.txt
├── participants.tsv
├── README
├── sub-01
│   ├── anat
│   │   └── sub-01_T1w.nii.gz
│   └── func
│       ├── sub-01_task-rest_run-01_bold.nii.gz
│       ├── sub-01_task-rest_run-01_events.tsv
│       ├── sub-01_task-rest_run-02_bold.nii.gz
│       └── sub-01_task-rest_run-02_events.tsv
└── task-rest_bold.json

Importantly, I need a bold image (sub-01_task-rest_run-01_bold.nii.gz), an anatomical image (sub-01_T1w.nii.gz) and an anatomical mask (sub-01_desc-brainmask_T1w.nii.gz).

To run docker with this data, I need to give docker access to the bids directory (in this case ds005). I can give docker access to ds005 through binding volumes. The option would look something like this: -v /path/to/ds005:/data

Furthermore, if I've cloned the repository and made some local changes to the code that I want to test in the docker container, I can bind the code directory to the docker container as well. The option would look like this: -v /path/to/RestingState:/opt/RestingState

Here is what the command would look like put together:

docker run -it \
-v /path/to/ds005:/data \
-v /path/to/RestingState:/opt/RestingState \
hbclab/restingstate \
  --epi=/data/sub-01/func/sub-01_task-rest_run-01_bold.nii.gz \
  --t1=/data/sub-01/anat/sub-01_T1w.nii.gz \
  --t1_mask=/data/derivatives/bet/sub-01/anat/sub-01_desc-brainmask_T1w.nii.gz \
  --roiList=/data/derivatives/data/roi_list.txt \
  --compcor

and if you didn't want to patch your local code in, just remove -v /path/to/RestingState:/opt/RestingState

docker run -it \
-v /path/to/ds005:/data \
hbclab/restingstate \
  --epi=/data/sub-01/func/sub-01_task-rest_run-01_bold.nii.gz \
  --t1=/data/sub-01/anat/sub-01_T1w.nii.gz \
  --t1_mask=/data/derivatives/bet/sub-01/anat/sub-01_desc-brainmask_T1w.nii.gz \
  --roiList=/data/derivatives/data/roi_list.txt \
  --compcor