FMRIPREP preprocessing

Tutorial

How to run a minimal preprocessing pipeline and extract the nuissance confounds with FMRIRPREP in the LAVIS' ADA HPCC.

Requirements

Singularity image

In order to run 'fmriprep' inside ADA, a singularity image of 'fmriprep' must have been created and uploaded to an accessible location. For this tutorial, the path of the singularity image is: /mnt/MD1200B/egarza/sfernandezl/singimages/fmriprep20190725.img

BIDS

FMRIPREP requires that the input data are organized according to the BIDS standard. Even though 'fmriprep' comes with its own validator. It's recommended to run a BIDS validator separately before running the script.

Data

For this tutorial, I'll be using a BIDS dataset of three subjects with two sessions of T1w, BOLD and epi fieldmap images:

Data
├── participants.tsv
├── sub-001
│   ├── ses-t0
│   │   ├── anat
│   │   │   ├── sub-001_ses-t0_T1w.json
│   │   │   └── sub-001_ses-t0_T1w.nii.gz
│   │   ├── fmap
│   │   │   ├── sub-001_ses-t0_epi.json
│   │   │   └── sub-001_ses-t0_epi.nii.gz
│   │   └── func
│   │       ├── sub-001_ses-t0_task-rest_bold.json
│   │       └── sub-001_ses-t0_task-rest_bold.nii.gz
│   └── ses-t1
│       ├── anat
│       │   ├── sub-001_ses-t1_T1w.json
│       │   └── sub-001_ses-t1_T1w.nii.gz
│       ├── fmap
│       │   ├── sub-001_ses-t1_epi.json
│       │   └── sub-001_ses-t1_epi.nii.gz
│       └── func
│           ├── sub-001_ses-t1_task-rest_bold.json
│           └── sub-001_ses-t1_task-rest_bold.nii.gz
├── sub-002
│   ├── ses-t0
│   │   ├── anat
│   │   │   ├── sub-002_ses-t0_T1w.json
│   │   │   └── sub-002_ses-t0_T1w.nii.gz
│   │   ├── fmap
│   │   │   ├── sub-002_ses-t0_epi.json
│   │   │   └── sub-002_ses-t0_epi.nii.gz
│   │   └── func
│   │       ├── sub-002_ses-t0_task-rest_bold.json
│   │       └── sub-002_ses-t0_task-rest_bold.nii.gz
│   └── ses-t1
│       ├── anat
│       │   ├── sub-002_ses-t1_T1w.json
│       │   └── sub-002_ses-t1_T1w.nii.gz
│       ├── fmap
│       │   ├── sub-002_ses-t1_epi.json
│       │   └── sub-002_ses-t1_epi.nii.gz
│       └── func
│           ├── sub-002_ses-t1_task-rest_bold.json
│           └── sub-002_ses-t1_task-rest_bold.nii.gz
└── sub-003
    ├── ses-t0
    │   ├── anat
    │   │   ├── sub-003_ses-t0_T1w.json
    │   │   └── sub-003_ses-t0_T1w.nii.gz
    │   ├── fmap
    │   │   ├── sub-003_ses-t0_epi.json
    │   │   └── sub-003_ses-t0_epi.nii.gz
    │   └── func
    │       ├── sub-003_ses-t0_task-rest_bold.json
    │       └── sub-003_ses-t0_task-rest_bold.nii.gz
    └── ses-t1
        ├── anat
        │   ├── sub-003_ses-t1_T1w.json
        │   └── sub-003_ses-t1_T1w.nii.gz
        ├── fmap
        │   ├── sub-003_ses-t1_epi.json
        │   └── sub-003_ses-t1_epi.nii.gz
        └── func
            ├── sub-003_ses-t1_task-rest_bold.json
            └── sub-003_ses-t1_task-rest_bold.nii.gz