The connectome pipeline automatically creates functional and structural connectomes from measured raw imaging data. Results are also packed in a way to be used directly within The Virtual Brain simulator software.
Please note that the software utilized for diffusion tractography (MRTrix) currently only supports single-shell diffusion data, i.e. dwMRI images recorded using only a single b-value for all different gradient directions.
The input data can be uploaded as a packed ZIP-container and must follow this simple folder-schema:
|-SUBJECT_ID
|—RAWDATA
|———BOLD-EPI
|————dicom1.dcm
|————dicom2.dcm
|———— ...
|———DTI
|————dicom1.dcm
|————dicom2.dcm
|———— …
|———MPRAGE
|————dicom1.dcm
|————dicom2.dcm
|———— …
Including BOLD-EPI data is optional. If you don’t include any BOLD data, the pipeline won’t produce functional connectivity matrix. Including DTI and MPRAGE data is mandatory i.e. the pipeline won’t work without those datasets.