Electrode Localization and Naming

First you will need to align the CT and MRI data so that when you find the coordinates of the electrodes with the CT, they match up to the fMRI surface you will use. This is done with

3dAllineate -base 3dsag_t1_2.nii -source {$ec}_CT+orig -prefix {$ec}CT_REGtoanat2 -verb -warp shift_rotate -cost mutualinfo -1Dfile {$ec}CT_REGtoanat2

You will then need to make a .tag file to record the position of the electrodes. If you have the electrocorticgraphy report or a picture from surgery, this is helpful to have when you start. Define the underlay as the CT_REGtoanat2 file and the overlay as the CT scan. It is easiest if you open SUMA and AFNI together for this. In AFNI, go to Define Data Mode, then plug-ins, then Edit Tagset. Using all three views, find the approximate center of the electrode. To record this location, first define the data set you are working with (CT_Regtoanat2), then name the file in the Tag File box (ex: HJelectrodes.tag). When you have to location you like, select one of the tags and press Set. "Add" will add more spots, "Set" sets that tag to the location you chose. If you have the data available, use the Tag Label Box to define each tag (ex: ch 32- Frontal 1), which is much easier than Tag #1, Tag #2, etc. Try to work in a systematic fashion. Using the SUMA view with the crosshairs (F3) will help. Make sure you press Write and Save frequently. Once you have this file, it is good to make a backup (cp electrodes.tag electrodebackup.tag).

Next you will need to make a .1D file for SUMA to read. It is open the .tag file in Excel to format it correctly. Delete the header row and the labels so that the file is just 3 columns of coordinates. On every row you will need to add 1 1 1 1 1.5 2 so that there are a total of 9 columns. These values are the RGB values and diameter of the electrode spheres. The top row of the file is #spheres. Copy all this over back to Text Editor, then save as .1D. In SUMA, press control+command+S and find the 1D file. You should see your electrodes as white spheres. In the full surface view, some electrodes may be underneath the surface.