Please go to https://andyrevell.github.io/implantRenders/ for the latest updates!

Made by Andy Revell (MD/PhD student at Penn)

Implant Links

Click to view implant:

Subjects
sub-RID0278	sub-RID0365	sub-RID0572
sub-RID0583	sub-RID0595	sub-RID0596
sub-RID0536	sub-RID0520

About

These renders show implantations of epilepsy patients. You can adjust your view using your mouse and control settings (see below image). Click on "Channels" to see the channel label names.

Metadata

Subjects	Implant	Sampling
sub-RID0278	SEEG	bilateral
sub-RID0365	SEEG	bilateral
sub-RID0520	SEEG + ECoG	left
sub-RID0536	SEEG	bilateral
sub-RID0572	SEEG	right
sub-RID0583	SEEG	left
sub-RID0595	SEEG	left
sub-RID0596	SEEG	left

SEEG: Stereoelectroencephalography ("toothpicks")

ECoG: Electrocorticography ("grids and strips")

Methods

Visual

Bullet Point Methods

See revellLab GitHub repository electrodeLocalization.py for example pipeline

1. Creation of brain 3D model

   • Data needed:
     • Pre-implant T1 image.
     • Preferably at 3T
     • Preferably using our high resolution 3T research protocol (not all patient acquire)
   • Software needed:
     • Freesurfer
     • Blender 3.9
     • Python 3.7+
     • Script blender_compress_mesh.py from revellLab GitHub repository
   • Step 1: Cortical surface reconstruction of brain
     • Software: Freesurfer
     • Command: recon-all -subjid ### -all -time -log logfile -nuintensitycor-3T -sd ### -parallel -threads 12
     • Takes about 1.5-2hrs for Andy's computer (AMD Ryzen 9 3900X 12-Core Processor, 64 GB RAM, Titan RTX GPU)
   • Step 2: Make 3D model
     • Convert lh.pial and rh.pial to scanner T1 space
       • Freesurfer command: mris_convert --to-scanner lh.pial lh.pial
     • Combine lh.pial and rh.pial AND convert to .stl 3D model file
       • reesurfer command: mris_convert --combinesurfs rh.pial lh.pial combined.stl
     • Convert to .stl to .glb file (To render on webpage using three.js)
       • Software: Blender 3.9
       • Use python script from revellLab GitHub repository
         • /packages/imaging/electrodeLocalization/blender_compress_mesh.py
       • Command: blender --background --factory-startup --addons io_scene_gltf2 --python blender_compress_mesh.py -- -i combined.stl -o brain.glb

2. Get implantation coordinates

   • Data needed:
     • Pre-implant T1 image (from above)
     • Coordinates in the pre-implant T1 space above
       • If coordinates in a different space, need the corresponding T1 image and register the pre-implant T1 image above
     • Optional: output of atlas localization pipeline to get tissue localization information of implant channels
   • Software needed:
     • FSL
     • Python 3.7+
   • Step 1: Register the pre-implant T1 image to the T1 image the coordinate file is in - skip if they are the same
     • Brain extract the images using FSL bet
     • Linear registration of the two images using FSL flirt
     • Apply the returned tranformation matrix from flirt to the coordinate file
       • FSL command: img2imgcoord -src ### -dest ### -xfm ### -mm ### > ###
       • See FSL's documentation of img2imgcoord for specific data sctructures files must be in
   • Step 2: Save coordinates in same location as the brain.glb file, name it electrodes.txt
     • electrodes.txt format
       • each row contains channel information. Column 1: Channel name; Column 2: x coordinate; Column 3: y coordinate; Column 4: z coordinate
       • Separation is a single space between columns (not comma or tab separated)

3. Get necessary files in single directory:

   • See example
   • File names:
     • brain.glb
     • electrodes.txt
     • index.html Get here
   • These three files are all you need, and the html file should work provided you name the .glb and .txt files accordingly
   • To run on local computer, follow these directions
     • I installed npm: npm install http-server -g (I forget if you need this to run the python -m http.server below)
     • python -m http.server
     • Type this into browser (I used Chrome, Firefox, and Microsoft Edge): http://localhost:8000/
     • The reason why you need the above is because web browser restrict loading of the 3D .glb files locally for security reasons.