General Notes¶

You should land on this page after collecting your fMRI data and converting it to BIDS. Here, you’ll find all the general information and FAQs about fMRI protocols.

Data Storage Suggestion

Bring a dedicated hard drive to the hospital for storing the output data. This will ensure that you have a reliable medium to transfer and secure the raw data from the scanner.

Where your data come from

MR11 (Siemens) sends DICOMs to XNAT (see Getting your data). The 7T is a GE scanner (see Flanders 7T). Notes for older Philips datasets are on the MR8 archive page.

Quick Links to Resources¶

These resources provide essential information and tutorials that can be consulted before or during your journey into SPM and fMRI analysis:

SPM Online Documentation - fMRI Tutorials: A very nice set of tutorials for functional MRI analysis using Statistical Parametric Mapping (SPM).
fMRI Prep and Analysis with Andrew Jahn: A ( The) YouTube channel offering tutorials on fMRI preprocessing and analysis, covering various aspects of neuroimaging.
SPM Programming Introduction: An introduction to programming with SPM.
SPM Manual: The official SPM manual, providing in-depth information on all aspects of SPM, from installation to advanced analysis techniques.
Introduction to SPM by Karl Friston: A brief guide to statistical parametric mapping, adapted from K. Friston’s 2003 introductory notes.

How to Store Raw Data¶

To avoid errors during BIDS conversion, store the raw data (e.g., data collected from the scanner, behavioral measures, eye-tracking) with the following folder structure:

sourcedata
└── sub-41
    ├── bh
    │   ├── 20240503104938_log_41-1-2_exp.tsv
    │   ├── 20240503105558_41_1_exp.mat
    │   ├── 20240503105640_log_41-2-1_exp.tsv
    │   ├── 20240503110226_41_2_exp.mat
    │   ├── 20240503110241_log_41-3-2_exp.tsv
    │   ├── 20240503110825_41_3_exp.mat
    │   ├── 20240503110851_log_41-4-1_exp.tsv
    │   ├── 20240503111433_41_4_exp.mat
    │   ├── 20240503111450_log_41-5-2_exp.tsv
    │   └── 20240503112032_41_5_exp.mat
    └── nifti
        ├── sub-41_WIP_CS_3DTFE_8_1.nii
        ├── sub-41_WIP_Functional_run1_3_1.nii
        ├── sub-41_WIP_Functional_run2_4_1.nii
        ├── sub-41_WIP_Functional_run3_5_1.nii
        ├── sub-41_WIP_Functional_run4_6_1.nii
        └── sub-41_WIP_Functional_run5_7_1.nii

Folder Structure

Ensure each subject’s data is organized as shown above to minimize errors during BIDS conversion. Store all behavioral and NIfTI files under sourcedata.

Handling NaNs in JSON Files¶

NaN values in JSON files can cause errors during the MRIQC workflow. To address NaN values, see the discussions in this post, this GitHub issue, and this NeuroStars thread.

Next Step → Set-up your environment