MRI data

Under construction

These pages are currently under construction.

Format summary

MRI data should be formatted according to BIDS. The full BIDS specification on MRI data can be found here.

Within the ANC, all data must be organized in a session directory, event if there is only one session. Take note of the following BIDS terminology: A session is a collection of data recordings, usually a single appointment during which a participant came to the scanner.

The MRI sequences are stored in .nii format accompanied by a corresponding .json file containing the metadata usually retrieved from the dicom header. These files are organisied within the session directory according to their data types. A scans.tsv file listing all acquired sequences must be added per session.

One crucial point is the file naming, as every sequence type has its very specific suffix, e.g. Blood-Oxygen-Level Dependent image is labeled _bold or a T1-weighted image like a MP-RAGE sequence is labeld T1w. Depending on the sequence type additional labels might be needed, for example the phase encoding direction of diffusion weighted images. For more information on the sequence naming see our guide on preparing MRI sequences. Also the required metadata within the .json file varies between sequence types. Tools for converting your raw data into BIDS format, for example BIDScoin, usually take care of this. Otherwise, please review the BIDS Documenation.

The data should be structured as follows:

└── MRI_Dataset/
    ├── README.md
    ├── dataset_description.json
    ├── participants.json
    ├── participants.tsv
    ├── task-nback_events.json
    └── sub-001/
        └── ses-01/
            ├── sub-001_ses-01_scans.tsv
            ├── anat
                ├── sub-001_ses-01_T1w.json
                └── sub-001_ses-01_T1w.nii
            ├── dwi
                ├── sub-001_ses-01_dir-PA_dwi.bval
                ├── sub-001_ses-01_dir-PA_dwi.bvec
                ├── sub-001_ses-01_dir-PA_dwi.json
                └── sub-001_ses-01_dir-PA_dwi.nii
            ├── fmap
                ├── sub-001_ses-01_phasediff.json
                └── sub-001_ses-01_phasediff.nii
            └── func
                ├── sub-001_ses-01_task-rest_bold.json
                ├── sub-001_ses-01_task-rest_bold.nii
                ├── sub-001_ses-01_task-nback_bold.json
                ├── sub-001_ses-01_task-nback_bold.nii
                └── sub-001_ses-01_task-nback_bold_events.tsv

Associated Data

If task data other then resting state was acquired during the scanning sequences, event files must be added. Thus see task experiment data.

It task data independent of the scanning sequences was acquired, also see task experiment data. This data should be added within the behavioral data directory beh.

If multiple sessions have been acquired, a sessions.tsv file should be added.