non-bids-data.md

Running the pipeline on non-BIDS data

We recommend you convert your data to BIDS format before running the pipeline. However, if you have non-BIDS data, you can still run the pipeline by following these steps:

• install the pre-requisites
• create a CSV file that describes the directory structure of your data
• run the pipeline using the CSV file

Create a CSV file

You will need to create an CSV file that describes the directory structure of your data.

The CSV file must contain one row for each subject you want to analyse. It must contain the following columns:

• flair: path to the FLAIR MRI image for a subject
• t1: path to the T1-weighted MRI image for a subject
• subject: the id of the subject these images belong to
• session: the id of the session these images belong to

For example, if you have the following directory structure:

data
├───subject-1-session-1
│   ├───flair.nii.gz
│   └───t1.nii.gz
│
├───subject-1-session-2
│   ├───flair.nii.gz
│   └───t1.nii.gz
│
├───subject-2-session-1
│   ├───flair.nii.gz
│   └───t1.nii.gz

you would create the following CSV file:

flair,t1,subject,session
subject-1-session-1/flair.nii.gz,subject-1-session-1/t1.nii.gz,1,1
subject-1-session-2/flair.nii.gz,subject-1-session-2/t1.nii.gz,1,2
subject-2-session-1/flair.nii.gz,subject-2-session-1/t1.nii.gz,2,1

Note

All filename must be relative to the data directory from which you run the Docker or Apptainer image. For example, with the above directory structure you would run the Docker (or Apptainer) run command from the data/ directory, and the paths in the CSV file must be relative to this directory.

Run the pipeline

To run the pipeline, follow the instructions for running the container, and pass the -l flag to the run command, specifying the relative path to your csv file. For example, to run with Docker:

docker run -v "${PWD}":/data hamiedaharoon24/enigma-pd-wml:<tag> -l input.csv

assuming you have saved the CSV file as input.csv in the data/ directory.

Output data

The pipeline will create a derivatives directory inside data/ containing the results. Your entire directory structure will look like this:

data
├── input.csv
├── enigma-pd-wml.log
├── subject-1-session-1
│   ├── flair.nii.gz
│   └── t1.nii.gz
│
├── subject-1-session-2
│   ├── flair.nii.gz
│   └── t1.nii.gz
│
├── subject-2-session-1
│   ├── flair.nii.gz
│   └── t1.nii.gz
│
├── derivatives
│    └── enigma-pd-wml
│          ├── QC
│          │   ├── PNGS/
│          │   ├── QC_guide_examples/
│          │   ├── dataset_1_ENIGMA_WML_QC_Linear_01.html
│          │   └── dataset_1_ENIGMA_WML_QC_Nonlinear_01.html
│          │
│          ├── sub-1
│          │   ├── ses-1
│          │   │   ├── input/
│          │   │   ├── output/
│          │   │   ├── sub-1_ses-1.log
│          │   │   └── sub-1_ses-1_results.zip
│          │   └── ses-2
│          │       ├── input/
│          │       ├── output/
│          │       ├── sub-1_ses-2.log
│          │       └── sub-1_ses-2_results.zip
│          │
│          ├── sub-2
│          │    └──ses-1
│          │       ├── input/
│          │       ├── output/
│          │       ├── sub-2_ses-1.log
│          │       └── sub-2_ses-1_results.zip
│          │
│          └── t1_volumes.csv

The session-level zip files are stored in data/derivatives/enigma-pd-wml/sub-1/ses-1/sub-1_ses-1_results.zip, and so on for the other subject / session ids. These are the files you will need to send to the ENIGMA-PD Vasc team.

The intermediate files are stored in the data/derivatives/enigma-pd-wml/sub-1/ses-1/input/ and data/derivatives/enigma-pd-wml/sub-1/ses-1/output/ directories for subject and session 1 (and the corresponding directories for other sessions and subjects).

The top-level log file is stored in data/enigma-pd-wml.log, and the session-level log files are stored in data/derivatives/enigma-pd-wml/sub-1/ses-1/sub-1_ses-1.log (and corresponding files for each subject / session combination).