mri2mne
Home FR

Start from a T1, without DICOM

You already have a T1 as NIfTI (de-identified, or from another tool) and not the original DICOM. The pipeline starts straight from that image.

Only one argument changes

Pass t1_path instead of dicom_dir. Exactly one of the two is required — passing both (or neither) raises an immediate error.

result = reconstruct_sources(
    subject="sample", output_dir="D:/derivatives",
    t1_path="D:/anat/sample_T1w.nii.gz",  # <- instead of dicom_dir
    eeg_file="D:/eeg/sample.edf",
    digitization="D:/dig/sample.elc",
    simnibs_bin_dir="C:/Users/me/SimNIBS-4.5/bin",
    events="find", event_id={"aud_l": 1},
)

The DICOM→NIfTI conversion is simply skipped; the T1 is copied as is and feeds charm. Every later stage is identical.

The supplied T1, as used for segmentation.
The supplied T1, as used for segmentation.