Beauchamp:ActivityMaps
From OpenWetWare
Jump to navigationJump to search
Make an activity map to show the percent gamma change on the brain surface:
- Extract percent gamma change values from Matlab. It should be a single column each row representing the average gamma activity recorded from an electrode. Call this file 'YAR_Gamma.txt' (YAR is an example subject ID here).
- In the afni folder of the corresponding subject ,open the ClosestProjected.do file. This file contains the electrode coordinates on the brain surface. Copy the coordinate values in a separate text file and call this file 'YAR_Elec.txt'.
- Concatenate the electrode coordinate values and gamma values such that the first 3 colums are the xyz coordinates and the forth column is the gamma values:
Both the YAR_Elec.tx and the YAR_Gamma.txt files should be in the afni folder of the subject.
cd afni 1dcat YAR_Elec.txt YAR_Gamma.txt> temp1.txt
Now temp1.txt contains the coordinate values for each electrode together with their gamma activity values.
- Dump the gamma values onto the electrodes:
Let's assume we have 32 electrodes
set electrode = 0 while ($electrode < 32) 1dcat temp1.txt'{'{$electrode}'}' > temp2.txt 3dUndump -prefix elec{$electrode} -datum float -master fs_SurfVol_Alnd_Exp+orig.BRIK -xyz -srad 5 temp2.txt @ electrode++ echo $electrode end
- Blur the gamma activity:
3dmerge -overwrite -prefix Gamma_Blurred -1blur_fwhm 1 -gnzmean elec*+orig.HEAD
All the electrodes will be combined in a single BRIK file called 'Gamma_Blurred+orig.BRIK.
- Show the activity map on the brain surface
- First load AFNI and SUMA together
cd .. ./@ec
- Click on the SUMA window and press Control+Command+s. Choose ClosestProjected.do to display the electrodes on the brain surface
- In the AFNI window set Underlay as fs_SurfVol_Alnd_Exp and Overlay as Gamma_Blurred