IntrAnat software

What is IntrAnat ?

 

(c) Inserm U1216 2012-2016 – Manik Bhattacharjee and 2014-2017 Pierre Deman
Software license : GNU GPL version 3

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

  • Multimodality and electrodes implantation 3D display and easy fusion between modalities. (MRI : T1, T2, FLAIR, fMRI, FGATIR, DTI; CT ; PET)
  • Semi-automatic estimation of the resection
  • 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 labbeling, and resection labelling.
  • Automatic exportation of dictionaries containing the total volume of the resection and percentage of MarsAatlas or Destrieux parcels which has been impacted by 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.
  • Read sEEG files (only Micromed © files for now) (and display the power (colormap) of a user specified band on electrode meshes in development)

The software is based on BrainVISA 4.5 (http://brainvisa.fr/web/index.html), Morphologist (http://brainvisa.fr/web/morphologist.html) and Cortical Surface (http://www.meca-brain.org/softwares/).

It’s using ANTs (http://stnava.github.io/ANTs/) and spm12 (http://www.fil.ion.ucl.ac.uk/spm/software/spm12/) for multimodality coregistration and spm12 for the estimation of the deformation field to convert into MNI Space.

The software is used on three project by the team: FORCE, NeuroPsyNov and F-Tract

User Documentation of the software : user_documentation.pdf

A new version of the software will be available september 2017 here: https://gin11-git.ujf-grenoble.fr/software_seeg/IntrAnat-Electrodes

Current status

IntrAnat is part of a research project involving Grenoble University Hospital, Grenoble Institute of Neurosciences and Lyon Neuroscience Research lab.

It is currently in development, so documentation may be lacking and many bugs are probably present.

This software must not be used for any medical purpose, but only as a tool to help researchers analyze the data.

THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

Screenshots

ImageImport : importation of a Nifti image (T1 pre-implantation)ImageImport_anon

Registration, normalization, AC-PC and brain segmentation by BrainVisa start here:

LocateElectrodes: display available anatomical data and enter electrode positions.

imageftractwebsite3

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

GroupDisplay :

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

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

imageftractwebsite2

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

plots_anon

mni1

Implantation of patients in the MNI. Right, result of a fMRI study generated in the MNI space using spm12. left fusion of the MNI T1 and the fMRI results. it helps to select patient cases according to the fMRI results of a cognitive task for example.

Display of the stimulation results of 4 patients

Below is a resume of how works the three IntrAnat Electrodes interface together.

ImageImport

ImageImport is used to add data to the database, register and normalize anatomical images.
Usual data includes T1 MRI before electrode implantation and T1 MRI or CT post-implantation. If a resection surgery is performed afterwards, a postOp T1 MRI may be stored in the database.

SEEG data can also be imported in the database (in development).

LocateElectrodes

LocateElectrodes is used to place SEEG electrode models onto the anatomy of the patients using post-implantation imaging (such as T1 MRI or CT). Available data can be displayed in the same window (such as brain hemispheres segmented by BrainVisa morphology toolbox)

ElectrodeEditor

A small software used to create electrode models and templates.

GroupDisplay

GroupDisplay is used to display electrodes of multiple patients in a common referential (currently only MNI space is supported).

Future tools

Displaying more data such as SEEG recordings in subject and template referentials.

Documentation

Documentation is available in the package in the doc directory. Two documents (in french) : user documentation and developer documentation. The UI is currently available in french only.

Currently user documentation is not in the package as some sensitive data was visible in the screenshots. Please contact us directly if you need more information.

Installation instructions

You must install BrainVisa 4.5.0, and either Matlab and SPM12, either ITK and ANTs first . IntrAnat is developped and used on GNU/Linux, but it should work on Apple OS X and Microsoft Windows too (however this is untested).

If you did not run BrainVisa before, run it, choose a database directory, run BrainVisa, import one MRI and create a protocol (e.g. “Epilepsy’) that IntrAnat will be able to use.

Decompress the archive, then make a link inside brainvisa-4.5.0/brainvisa/toolboxes/ to the epilepsie-toolbox directory in IntrAnat directory.

Copy electrode templates from IntrAnat directory (all .elecdef files) in a directory called “electrode_models” in the BrainVisa database/Epilepsy directory. Then run BrainVisa, select the process Data Management/Update Databases and run it.

Open a terminal, cd to IntrAnat directory, type “source /my/path/toBrainvisa/bin/bv_env.sh” to setup brainvisa paths, then  “python ImageImport.py”, or “python locateElectrodes.py” or “python groupDisplay.py” to run the software.

Download

Download available on demand. Contact Manik Bhattacharjee or Pierre Deman

2014-07-30 release