IntrAnat Electrodes

A software to visualize electrodes implantation on image data and prepare database for group studies.

  • Multimodality and electrode implantation with 3D display and easy co-registration between modalities. (MRI : T1, T2, FLAIR, fMRI, DTI; CT ; PET)

  • Semi-automatic estimation of the volume of resection

  • Importation of SEEG files (for now only .TRC, Micromed©)

  • Display of cortico-cortical evoked potential mapping

  • Automatic exportation of "dictionaries" containing the information of contact positions in the native and MNI coordinate systems, associated parcels in different atlas (MarsAtlas, Destrieux – Freesurfer, Brodmann, AAL, etc.), white/grey matter labeling, and resection labeling.

  • Automatic exportation of dictionaries containing the total volume of the resection and percentage of MarsAtlas or Destrieux parcels which have been considered by the resection (for now only assumes no brain deformation due to the resection).

  • Display of Epileptogenicity maps coregistered with other modalities (all statistical maps registered in the T1 pre space are loadable).

  • groupDisplay can be used to visualize electrode contacts from many patients over images in the MNI referential and to research patients according to different keywords.

IntranatElectrodes software is based on BrainVISA, Morphologist and Cortical Surface. It uses ANTs and spm12 for multimodality coregistration and spm12 for estimation of the deformation field to convert into MNI Space. It needs a Matlab license to run the normalisation and groupDisplay interface.

The software can be found here:

Installation instruction can be found on the wiki page of the git project.

In the folder where you save the codes, you have to unzip the following file: MNI_parcels

You can download a defaced database as example: Defaced_Database

Locate Electrodes Interface (patient referential):


Example of visualization done with locateElectrodes

a: MarsAtlas parcesl with 3d implantation and resection mesh (in blue). b: PET with 3d electrodes and resection mesh (in grey). c: fusion of the 3DT1 and the Fiber Numbers from DTI, and 3d electrodes.

d: fMRI results (statistical map over anatomical MRI) on the left and PET on the right, with 3d electrodes implantation. e: on the left, 3DT1 fusioned with resection mask, on the right 3DT1 fusioned with Epileptogenicity Index map.

1: Excel file with stimulation report. 2: Results of the stimulation, color code is: grey bipole not stimulated, black stimulated and no response, red patient reported a "seizure like sensation", blue patient reported a sensation different from the one during the seizure.

3: Results of the stimulation: color code is: grey bipole not stimulated, black stimulated but no response, color sensation according to the classification on the excel file (motor, sensitive, sensory, vegetative, emotional, experiential, superior function), white is multiple sensation

Group Display Interface:

The first window allows to research patient according to different criteria:

Example of research criteria available in the latest version of the software:

The second window is the glass brain visualization (using MNI position of the contacts):

Display of the stimulation results of 4 patients.

Figure summarising how IntrAnat Electrodes software works


The software presented on this page is for research purpose only.
It is provided "as is," Inserm and its collaborators do not assume any liability or responsibility for its use.