Category: Brain Stuff

Freesurfer Brain and SEEG Electrodes in CURRY

Importing Freesurfer pial surface into CURRY gives great visual representation of SEEG electrode locations. In the figure above, the screenshot was taken of a left lateral view of the pial surface model and then copied into PowerPoint where the labels were added.

In CURRY 8 you can import Freesurfer segmentation results such as the pial surface (lh.pial and rh.pial) files. You will need to co-register the Freesurfer files using the T1.mgz image data file.

To import your Freesurfer anatomy files into CURRY follow these steps:

  1. You will need lh.pial, rh.pial & T1mgz.
  2. Add T1.mgz to (Insert Image Data File) to the patient study
  3. Switch to Freesurfer coordinates (Freesurfer, NiftTi (R,A,S)
  4. Go to the Results panel, right-click on Surfaces and load lh.pial, hit OK.
  5. Hit No when asked to Add color intensity.
  6. CURRY will then ask you if you want to load the contents of rh.pial. Hit Yes.
  7. When finished, you should see lh.pial rh.pial in the Results and Objects list. Both left and right hemispheres have been combined.
  8. You now have your Freesurfer brain.

Vulnerabilities Discovered in Natus Xltek NeuroWorks Software

ICS-CERT issued an advisory following the discovery of 8 vulnerabilities in Natus NeuroWorks v8.

If the vulnerabilities are exploited they can allow a malicious hacker to crash the vulnerable device or trigger a buffer overflow condition that would allow remote code execution.

You should update your version of Neuroworks to 8.5 GMA 3 or later. It is available free of charge for users of NeuroWorks/SleepWorks Version 8.0, 8.1, 8.4, or 8.5. The Natus Neuro technical support department should be contacted for further information or download here.

SEEG/ECOG electrode locations in Brainstorm

Localization of intracranial electrodes is critical for invasive epilepsy evaluations and to confirm or not confirm the epileptic zone hypothesis. Various methods exist using various open-source and commercial software. Here is one method using some latest updates to the Brainstorm software.

Required imaging:

  • Pre-implantation T1 without contrast 1mm 3D volume scan
  • Post-implantation CT scan without contrast 1mm 3D volume scan

Assuming you are already familiar with Brainstorm and have already created anatomy files using Freesurfer:

Import Freesurfer anatomy

Choose Freesurfer folder

Change file type to Freesurfer

Set fiducial points & compute MNI coordinates

Convert CT to .nii.gz first with MRIcroGL (drag and drop)

Import CT by selecting ‘Import MRI’

Select the CT .nii file

Apply transformation

Register

Register on default MRI

CT overlay in MRI Viewer

Import ECOG data

Edit channel file

Change channel type to ECOG

Go to CT, Display, Overlay on default MRI (MRI Viewer)

Right click, Electrodes, Set electrode position

View in 3D

http://neuroimage.usc.edu/brainstorm/

 

Freesurfer Guide (Mac)

FreeSurfer is an open source software suite for extracting the cortex from an MRI, and more.

I’m using Brainstorm, but Brainstorm cannot extract the cortex from the MRI so I need to do this with FreeSurfer. There are also other utilities like BrainSuite that can do this as well.

Step 1

Download Freesurfer here.

Step 2

Register for a license key here.

Step 3

Follow the installation instructions. Create a license.txt file, copy the key into it and save in the freesurfer folder.

Sourcing FreeSurfer Mac from terminal:

$> export FREESURFER_HOME=/Applications/freesurfer
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh

Step 4

Navigate to your DICOM folder in terminal.

Run the recon-all command

recon-all -i file.dcm -subject NAME -all

Where file.dcm should be one of the DICOM files in your folder (e.g. 00000001.dcm or just 00000001). Freesurfer will automatically get the rest of the images in the series.

After the -subject argument NAME should be the name you want to call the study/subject. There will be a folder created with this name in the Applications/FreeSurfer/Subjects folder.

The process can take 10-20 hours, for me, it took ~10hrs on my 2011 core i5 Macbook Pro.

screen-shot-terminal-freesurfer

Once it is done you can proceed to import your Freesurfer anatomy into Brainstorm. See the tutorial here.