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Welcome to the IntrAnat wiki!

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

https://f-tract.eu/software/intranat

• 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 for now a Matlab license to run the normalisation and groupDisplay interface.

How to install

There are two main options at the moment

• Use Docker. We created a (very large) docker image that contains all necessary dependencies. On a linux distribution such as Ubuntu 16.04, install docker with sudo apt-get install docker.io. Then run docker pull demanp/intranat:release. Create a directory to store Brainvisa and Intranat database on your computer. If your user is called USER, create /home/USER/BvDatabase Then you need to run the docker image with a number of options that allow OpenGL to work with docker :

docker run -u USER -it -v /home/USER/BvDatabase:/casa/BvDatabase -v /home/USER/.ssh/id_rsa:/home/user/.ssh/id_rsa -v /home/USER/.ssh/id_rsa.pub:/home/user/.ssh/id_rsa.pub --net=host -v /tmp/.X11-unix:/tmp/.X11-unix -e QT_X11_NO_MITSHM=1 --privileged -e DISPLAY=$DISPLAY -v /usr/share/X11/locale:/usr/share/X11/locale:ro demanp/intranat:release /bin/bash

If > -u USER doesn't work, try replacing by > -u id -u:id -g

In the container, run cd /usr/local/IntrAnat, then python ImageImport.py, or python locateElectrodes.py according to the software you want to run.

For now IntrAnat as a matlab dependencies, so you have to mount matlab from your host machine into the docker image: https://hub.docker.com/r/ninjaben/matlab-support/ we are working to remove this dependicy but it's not ready yet

If you want to use a sample dataset, download the "defaced database" at the end of this page, uncompress it into your local database /home/USER/BvDatabase, then run the docker container, start "brainvisa" command, choose the "Data Management" toolbox, double*click on the "Update Databases", the /casa/BvDatabase should be selected, then click on the "update" button. This allows brainvisa to index the data you added into its database directory. You can now close brainvisa. You can then run cd /usr/local/IntrAnat, then python ImageImport.py, or python locateElectrodes.py according to the software you want to run.

• Install manually.

  • Clone this repository.
  • Uncompress this file in the git folder (if the link doesn't work please look at this page)
  • Checkout brainvisa_4.6 branch
  • Download and install Brainvisa 4.6
  • Inside the brainvisa installation, in the brainvisa/toolboxes directory, create a symbolic link to IntrAnat/epilepsy-toolbox called epilepsy.
  • Inside the brainvisa installation, in the shared/brainvisa-shared directory, create a symbolic link to IntrAnat/electrode_models.
  • Run Brainvisa and update the databases (in data management toolbox / update databases, but it should open automatically the first time you run brainvisa)
  • In Brainvisa preferences, in the database section, add a directory on your computer to use as the main database for your data
  • Install Freesurfer, ANTs, Matlab (they must be in the PATH) and SPM12 (must be available in matlab standard path)
  • In a terminal, run source BRAINVISA_INSTALL/bin/bv_env.sh; cd INTRANAT_INSTALL; python ImageImport.py

• Defaced Database A defaced Database can be found here. (if the link doesn't work please look at this page.)

How to use it

Please read the user documentation.