iEEG/ECoG study, it is very common to localize the electrodes using ‘CT’ scans. The CT images have different orientations to the MR images, hence co-registration is often needed. This package does not provide co-registration functions, as different labs might have different approaches.
threeBrain only takes co-registered CT scans and visualize them directly. Therefore if you have already co-registered CT, skip the next part.
The rest part of this article uses
N27 sample files mentioned by the previous vignette. If you are using this example, please execute the following R code to set up. Alternatively, you can substitute variables
library(threeBrain) <- "N27" subject_code <- "~/Downloads/N27" subject_path <- freesurfer_brain2(subject_path, subject_code)brain
(skip if you have generated co-registered CT in ‘Nifti’ formats)
This part provides one working method via
FLIRT packages. Again, other methods will work as long as they output CT aligned to MRI in ‘Nifti’ formats.
Step 1: Merge all
DICOM images to
Open your terminal (
power shell), change directories to where
DICOM images are, and run
dcm2niix [folder with DICOM images]
Do the same to
T1 MR images too.
Step 2: Copy the two
.nii files generated in the previous step to a same folder, rename them to be
flirt -in ct.nii -ref t1.nii -out ct_in_t1.nii -omat ct2t1.mat -interp trilinear -cost mutualinfo -dof 6 -searchcost mutualinfo -searchrx -180 180 -searchry -180 180 -searchrz -180 180
There will be a
ct_in_t1.nii file generated.
Assuming you have generated co-registered CT scans in file
ct_in_t1.nii, please copy it to the subject folder. The file should be located at
Next, type in and change the file path to
ct_in_t1.nii just created
<- file.path(subject_path, "mri/ct_in_t1.nii") ct_path ::localization_module(subject_code = subject_code, threeBrainfs_path = subject_path, ct_path = ct_path)
You will see the threshold CT displayed along with the pial surfaces.
Edit Mode (in the
Electrode Localization panel) is
CT/Volume. Now move your mouse cursor to the green electrodes, the localization control panel will display the
T1 (native RAS coordinate), and
MNI305 (‘MNI’ template coordinate). Double-click on the green areas, and a new electrode will be created.
The default threshold of CT scans is set to 3000. However, this threshold might need to be adjusted in order to achieve high accuracy. The following figures demonstrate the results of different threshold.
If the threshold is too low, then other irrelevant structures will appear. If the threshold is too high, some electrodes might disappear.
To adjust the CT threshold, open the
Volume Settings from the control panel, slide
When electrodes are too small, or the CT is unavailable, electrode localization can be done on the MR images. Localization via MRI can be done by the following steps:
Edit Mode(in the
Electrode Localizationpanel) to
Volume Settingspanel, enable
Overlay Axial, or
Sagittalplane to desired position
In most of the scenarios, electrodes form grids or strips, The
threeBrain provides interpolation functions.
For example, we want to localize the electrodes circled in orange color (top-left). You could of course mark them one by one. More efficiently, you can simply localize the electrodes at both ends, set the
Interpolate Size to 6 (there are 6 more electrodes to be added), make sure there is no other objects blocking the sight, and hit the
Interpolate from Recently Added button (circled in the figure). All other electrodes will be automatically generated.
The newly added electrodes might be inaccurate. Don’t worry, you can adjust them later!
Once all the electrodes are marked, change
Edit Mode to
refine. In the refine mode, you can
Enable/Disable Electrode, the electrode will be disabled/enabled. The disabled electrode will be colored in gray.
To automatically adjust all electrodes, simply click
Auto-Adjust All. The new electrode locations will be calculated via a weighted average.
To automatically adjust a specific electrode, double-click one electrode. The highlighted electrode will be colored in red. Then click on
To manually adjust a electrode, double-click one electrode. The highlighted electrode will be colored in red. Then hover the mouse above the canvas, press and hold keyboard
shift+1 to move the electrode along
Right/Left axis. Press and hold
shift+2 to move the electrode along
Anterior/Posterior axis. Press and hold
shift+3 to move the electrode along
Once Finished electrode localization, you can take screenshots by opening
Default panel, and click on
To download electrode table, click on
Download as csv in the
Electrode Localization panel. The electrode table should look as follows:
You will notice that the
Electrode column is left blank. This is because localization order might be different than the recording channel number. Please fill out
Electrode column as the actual channel number (integers).