BIDS_EEG-fMRI

Scripts to process and organize the EEG-fMRI dataset

1. Organizing the dataset

Each subject MUST have the following organization, where /maps contains the result of the peak maps analysis derived from the EEG-fMRI registered to the fisrt run of /anat/<sub>_T1w.nii.gz or /anat/<sub>_run-1_T1.nii.gz

sub-ep1586
├── anat
│   ├── sub-ep1586_T1w.json
│   └── sub-ep1586_T1w.nii.gz
├── fmap
│   ├── sub-ep1586_magnitude1.json
│   ├── sub-ep1586_magnitude1.nii.gz
│   ├── sub-ep1586_magnitude2.json
│   ├── sub-ep1586_magnitude2.nii.gz
│   ├── sub-ep1586_phasediff.json
│   └── sub-ep1586_phasediff.nii.gz
├── func
│   ├── sub-ep1586_task-spike_run-1_bold.json
│   ├── sub-ep1586_task-spike_run-1_bold.nii.gz
│   ├── sub-ep1586_task-spike_run-1_events.tsv
│   ├── sub-ep1586_task-spike_run-2_bold.json
│   ├── sub-ep1586_task-spike_run-2_bold.nii.gz
│   └── sub-ep1586_task-spike_run-2_events.tsv
└── maps
    ├── sub-ep1586_space-T1w_desc-type01_fdr04p92_EEG-fMRI.nii.gz
    ├── sub-ep1586_space-T1w_desc-type01_usedhrf_EEG-fMRI.nii.gz
    ├── sub-ep1586_space-T1w_desc-type02_fdr04p66_EEG-fMRI.nii.gz
    ├── sub-ep1586_space-T1w_desc-type02_usedhrf_EEG-fMRI.nii.gz
    ├── sub-ep1586_space-T1w_desc-type03_fdr04p51_EEG-fMRI.nii.gz
    └── sub-ep1586_space-T1w_desc-type03_usedhrf_EEG-fMRI.nii.gz

2. Processing with micapipe

Example: how to run one subject locally

The first positional argument MUST be the subject ID with the string sub-. The second positional argument MUST be the FULL subjects's MICs freesurfer ID. (e.g. sub-PX000_ses-01)

sub=sub-ep1586
mics=sub-PX005_ses-01
singularity_micapipe_EEG-fMRI.sh "${sub}" "${mics}"

Example: how to run one subject on the mica.q (SGE)

sub=sub-ep1586
mics=sub-PX005_ses-01
logs=/data_/mica2/tmpDir/"${sub}"

qsub -q mica.q -pe smp 10 -l h_vmem=6G -N "${sub/sub-/}" -e "${logs}".e -o "${logs}".txt \
/<full path to>/BIDS_EEG-fMRI/functions/singularity_micapipe_EEG-fMRI.sh "${sub}" "${mics}"

3. Sample all peak maps to surface

micapipe structural processing MUST have been successfully run before this step.

sub=sub-ep1586
/<full path to>/BIDS_EEG-fMRI/functions/map2surf.sh "${sub}"