Beauchamp:Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)

Also see: Beauchamp:Electrode Localization and Naming

Step 1: Get the MR and CT scans of the patient

Step 2: Create a patient folder on the server i.e. /Volumes/data/UT/YAR (YAR is the patient ID in this example case) Copy in MR and CT scans with OsiriX, then export the images to the patient's folder. Choose Hierarchical and Decompress DICOMs options during the export. Take out the spaces in MR and CT folder names. The folder names should look like as follows:

/Volumes/data/UT/YAR/LastName_FirstName_MR/MRBRAINWITHOUTCONTRAST
/Volumes/data/UT/YAR//LastName_FirstName_CT/CTBRAINWITHOUTCONTRAST

Step 3: Process anatomical MR data:

In terminal window type:

set ec = YAR 
set session = /Volumes/data/UT/YAR/afni 

This way the processed anatomical files will be saved in the afni folder under the patient's directory.

There should be two different T1 scan folders in the MRBRAINWITHOUTCONTRAST folder. These folders are usually named T1_TFE_NSA01 (include images from 1st T1 scan) and T1_TFE_NSA02 (include images from 2nd T1 scan). We use the images in these folders.

• Create 3D datasets for use with AFNI from these 2D MR image files

For the 1st T1:

cd /Volumes/data/UT/YAR/LastName_FirstName_MR/MRBRAINWITHOUTCONTRAST/T1_TFE_NSA01
to3d -session $session -prefix {$ec}anatr1 IM-0011-0*  

For the 2nd T1:

cd /Volumes/data/UT/YAR/LastName_FirstName_MR/MRBRAINWITHOUTCONTRAST/T1_TFE_NSA02
to3d -session $session -prefix {$ec}anatr2 IM-0012-0* 

• Align the 1st T1 to the 2nd T1

This takes approximately 7 minutes.

cd /Volumes/data/UT/YAR/afni (YARanatr1 and YARanatr2 are in afni folder)
3dAllineate -base YARanatr2+orig -source YARanatr1+orig -prefix ${ec}anatr1_1RegTo2 -verb -warp shift_rotate -cost mi -automask -1Dfile ${ec}anatr2toanatr1

• Average the two aligned T1s into one dataset

This takes approximately 30 seconds.

3dmerge -gnzmean -nscale -prefix ${ec}anatavg ${ec}anatr2+orig  ${ec}anatr1_1RegTo2+orig

Step 4: Make the surface model

• Create an 'fs' directory under the patient's directory to save the surface files from freesufer

/Volumes/data/scripts/@prep_dir {$ec}anatavg+orig.BRIK

• Create different cortical surfaces in Freesurfer (i.e. inflated surface, pial surface, white matter surface etc.)

This step takes several hours. It also creates sulc files that contain information about the displacement of sulci and gyri from a hypothetical averaged surface.

/Volumes/data/scripts/@recon {$ec}anatavg+orig.BRIK 

• Convert Freesurfer files to to gift format that is readable by SUMA.

Align newly made Freesurfer surfaces to the original experiment anatomy made by AFNI.

/Volumes/data/scripts/@finish {$ec}anatavg+orig.BRIK  

This step basically runs @SUMA_Make_Spec_fs to make a SUMA directory under the fs directory and saves the .gii format surface files in this directory. It creates fs_both.spec file that contains the surface specifications. It also runs @SUMA_AlignToExperiment and generates the fs_SurfVol_Alnd_Exp file.

• Make pial-outersmoothed surfaces in Freesurfer

set subjid = fs
set SUBJECTS_DIR = /Volumes/data/UT/YAR
setenv SUBJECTS_DIR /Volumes/data/UT/YAR
set ec = fs
recon-all -s $ec -localGI

This step creates pial_outer_smoothed and pial_lgi surfaces under fs/surf directory.

• Update the SUMA directory to reflect the changes

cd fs
@SUMA_Make_Spec_FS -GIFTI -sid fs

This step adds the newly made pial_outer_smoothed and pial_lgi surfaces in the SUMA directory in .gii format.

• Create skull stripped anatomy to allineate to the EPI

EPI images do not cover the skull. EPI and T1 match better if we crop the skull from the T1 images as well.

This takes approximately 3 minutes.

cd /Volumes/data/UT/YAR/afni
set ec = YAR
3dSkullStrip -input {$ec}anatavg+orig -prefix {$ec}anatavgSS  

• Transform the skull stripped anatomical image to match a template in TLRC space

This takes approximately 3 minutes.

@auto_tlrc -base TT_N27+tlrc -no_ss -input {$ec}anatavgSS+orig  

Step 5: Process CT data:

• Create 3D datasets for use with AFNI from these 2D CT image files

set ec = YAR
set session = /Volumes/data/UT/YAR/afni
cd /Volumes/data/UT/YAR/LastName_FirstName_CT/CTBRAINWITHOUTCONTRAST/Axial__Supine_Scan_3 
to3d -session $session -prefix {$ec}_CT IM-0001-0*

Step 6: Align the CT to the T1:

In this step use the 2nd T1 (YARanatr2+orig) as the base.

3dAllineate -base YARanatr2+orig -source {$ec}_CT+orig -cmass -prefix {$ec}CT_REGtoanat2 -verb -warp shift_rotate -cost mutualinfo -1Dfile {$ec}CT_REGtoanat2

- In afni display YARanatr2 as underlay and YARCT_REGtoanat2 as overlay to check if the alignment worked well.

Step 7: Locate the electrodes on the brain

• Tag the Electrodes

- Load AFNI and SUMA together

cd /Volumes/data/UT/YAR
set ec = YAR
./@ec

- In afni set underlay to fs_SurfVol_Alnd_Exp+orig and overlay to YARCT_REGtoanat2

Setting the background to overlay to see just see the CT scan sometimes makes it easier to see the electrodes. 'u' key can be used to switch the background between underlay and overlay.

- Go to Define Datamode --> Plugins --> Edit Tagset

- Set Dataset as fs_SurfVol_Alnd_Exp

- Name Tag File as YARelectrodetags.tag

- Find the densest view of an electrode, make sure it's centered in all views (axial, saggital and coronal) and press 'Set' and then 'Save'

- Press 'Write' once all the electrodes are tagged. This will write the YARelectrodetags.tag file and save it in the afni folder.

- Open the tag file YARelectrodes.tag in Excel and re-order the electrode tags in the order of the channel numbers

- Make a copy of YARelectrodes.tag with the file name extension .1D

cp {$ec}electrodetags.tag {$ec}electrodetags.1D

- Open in {$ec}electrodetags.1D in Excel and edit the file so that it only has the 3 columns of x,y,z

• Project the tagged electrodes onto the closest node on the pial-outer-smoothed surface

SurfaceMetrics -spec /Volumes/data/UT/YAR/fs/SUMA/fs_both.spec -sv fs_SurfVol_Alnd_Exp+orig -surf_A lh.pial-outer-smoothed.gii -closest_node YARelectrodetags.1D -prefix {$ec}ClosestNodes_pialenvelope

- Open YARClosestNodes_pialenvelope.1D.dset in Excel and copy 3 columns of Xn, Yn, Zn coordinates. Paste Xn, Yn, Zn coordinates in a new Excel sheet and enter #spheres in the first cell of the document and format it as follows:

Xn Yn Zn 1 1 1 1 1.5 2.2

Electrode color is black for [0 0 0] and white for [1 1 1]. Electrode size is 1.5 for regular, 0.5 for mini electrodes.

- Save it as YARClosestProjected.txt and copy is as a .do file

cp {$ec}ClosestProjected.txt {$ec}ClosestProjected.do

• Display the projected electrodes on the brain surface

- Open "Select Displayable Objects File" shell by pressing "Comman & Control & s" on the keyboard. Set filter in shell to *do and select the appropriate .do file.

HINTs to make electrode tagging easier:

1) Display electrodes on the brain surfer in SUMA window

- Load AFNI and SUMA together by the ./@ec command

- Set underlay to fs_SurfVol_Alnd_Exp+orig and overlay to YARCT_REGtoanat2

- Increase the threshold so that in the SUMA window, electrodes look as colorful spots on the gray brain surface. Right clicking on these colorful spots on the SUMA window will take the Xhairs to the corresponding electrode position in the AFNI display window.

2) Display electrodes on the brain by using AFNI C Renderer

- Go to Define Datamode --> Plugins --> Render Dataset

- Choose YARanatSS as underlay and YARCT_REGtoanat2 as overlay

- Select See Overlay and DynaDraw. Increase the threshold so that everthing on the brain surface doesn't look green. Hit automate to generate the surface image with electrodes on it

- Play with the Roll, Pitch and Raw values to see the brain surface from different views

- Select See Xhairs. This way the Xhairs in the rendering window will move together with the Xhairs in the AFNIdisplay window

Step 8: Label the electrodes

- Go to Define Datamode --> Plugins --> Edit Tagset

- Load the electrode tags with the same dataset setting (fs_SurfVol_Alnd_Exp)

- Enter a Tag Label for each electrode and press 'Relabel' and 'Save'

- Press 'Write' after relabeling all the electrodes

• In Matlab, generate a generateOBJSetting.m script for the subject with the channel list.

• Generate a YAR_Label_Input.txt file with the closest projected x,y,x coordinates and run the read_write_elec_labels.m script.

• Copy the generated YAR_ElectrodeLabels.niml.do file into the patient's afni folder and paste the following line at the beginning of the file:

<nido_head													
coord_type	=	mobile											
default_SO_label	=	CURRENT		
bond	=	none	
/>	

Electrode labels can now be displayed on the brain surface next to the corresponding electrodes. In SUMA window, "Select Displayable Objects File" shell by pressing "Command & Control & s" on the keyboard. Set filter in shell to *do and select the appropriate .do files that correspond to the electrode locations (i.e. YARClosestProjected.do) and electrode labels (i.e. YAR_ElectrodeLabels.niml.do).