Beauchamp:ALICE
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This page shows the steps used by the ALICE package to localize electrodes. These steps are called from within a Matlab GUI.
The GUI has three steps.
Here is the log file from the first step (an edited version of /Volumes/data/UT/YBK/ALICE/log_info/Step1_log.txt with comments added )
MRI scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/MRI/YBK_T1.nii
FS segmentation selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/FreeSurfer/t1_class.nii
This file was originally called YBK_fs_ribbon_rh_class.nii (renamed version of rh.ribbon.nii)
CT scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/CT/CT_highresRAI.nii
This file was originally called YBK_CT.nii
Aligning CT to MRI... This might take several minutes. Please wait... tcsh -x alignCTtoT1_shft_res.csh -CT_path CT_highresRAI.nii -T1_path../MRI/YBK_T1.nii
This shell script contains the following steps:
@Align_Centers -base $t1 -dset $ct 3dresample -input CT_highresRAI_shft.nii -prefix CT_highresRAI_res_shft.nii -master $t1 -dxyz 1 1 1 -rmode NN align_epi_anat.py -dset1 $t1 -dset2 CT_highresRAI_res_shft.nii -dset1_strip None -dset2_strip None -dset2to1 -suffix _al -feature_size 1 -overwrite -cost nmi -giant_move -rigid_body > status.txt 3dcopy CT_highresRAI_res_shft_al+orig CT_highresRAI_res_al.nii 3dcopy $t1 ./temp_ANAT.nii afni -com "SWITCH_UNDERLAY temp_ANAT.nii" -com "SWITCH_OVERLAY CT_highresRAI_res_al.nii"
The log file from the second step does not contain the called commands, the list below has been extracted from the Matlab file ctmrGUI.m
Three parameters are set in the GUI: electrode max intensity, electrode volume, inter electrode space.
For subject YBK, the max intensity that worked best was 3500. Electrode volume was set to “2”, space was set to “1”.
The GUI then calls this script:
([tcsh -x 3dclustering.csh -CT_path ../CT/CT_highresRAI.nii -radius ' num2str(obj.settings.R) ' -interelectrode_space ' num2str(obj.settings.IS) ' -clip_value ' num2str(obj.settings.CV)]);
This script contains the following commands:
3dclust -savemask 3dclusters_r${r}_is${is}_thr${cv}.nii -overwrite -1Dformat -1clip $cv $is $r $ct > clst.1D
# make sure the clusters all show up in afni with distinct colors
3drefit -cmap INT_CMAP 3dclusters_r${r}_is${is}_thr${cv}.nii
# now resample the clusters, erode, dilate and cluster again
# this helps separate the clusters that overlap
3dresample -prefix temp_clusts_rs0.5 -overwrite -rmode NN -dxyz 0.5 0.5 0.5 -inset 3dclusters_r${r}_is${is}_thr${cv}.nii
3dmask_tool -dilate_inputs -1 +2 -prefix temp_clusts_rs0.5_de2 -overwrite -inputs temp_clusts_rs0.5+orig
3dclust -savemask 3dclusters_r${r}_is${is}_thr${cv}.nii -overwrite -1Dformat -1clip $cv $is $r temp_clusts_rs0.5_de2+orig > clst.1D
3drefit -cmap INT_CMAP 3dclusters_r${r}_is${is}_thr${cv}.nii
rm temp_clusts*.HEAD temp_clusts*.BRIK*
IsoSurface -isorois+dsets -mergerois+dset -autocrop -o_gii 3dclusters_r${r}_is${is}_thr${cv}.gii -input 3dclusters_r${r}_is${is}_thr${cv}.nii
echo "Clustered dataset saved as 3dclusters_r${r}_is${is}_thr${cv}.nii"
echo "Table of coordinates saved as clst.1D"
Afni and SUMA were opened using this script:
(['tcsh -x open_afni_suma.csh -CT_path ../CT/CT_highresRAI.nii -clust_set ' clust_set ' -clust_surf ' clust_surf ], '-echo')
The script contains the following commands:
# script to write out electrode positions
# assumes one has previously run this previous script and created the roi surfaces for all the electrodes
# with these commands
# tcsh @3dclustering -CT_path CT.nii -radius 4 -interelectrode_space 3 -clip_value 2999
# IsoSurface -isorois+dsets -mergerois+dset -autocrop -o_gii 3dclusters.gii -input 3dclusters_r?_is?.nii
set PIF = DriveAfniElectrodes #A string identifying programs launched by this script
@Quiet_Talkers -pif $PIF #Quiet previously launched programs
#Get a free line and tag programs from this script
set NPB = "-npb `afni -available_npb_quiet` -pif $PIF -echo_edu"
echo $NPB > ecognpb.txt
set surfcoords = "surf_xyz.1D" # record the electrode positions in a text file - this one gets the position at the surface
#set surfcoords_i = "surf_ixyz.1D" # record the electrode positions in a text file - this one gets the position at surface with index
set sumasurf = lastsurfout.txt
set ct = "CT+orig"
set clust_surf = "3dclusters.gii"
set clustset =
####### START new code for el cluster shading v2.0 (MPBranco 300617)###########################
set clust_surf_base = `basename -s .gii $clust_surf`
set clust_niml_set = ${clust_surf_base}.niml.dset
rm lastsurfout.txt temproilist.txt
# make a temporary copy of the coloring dataset to recolor as we go
set nlabels = `3dinfo -labeltable $clust_niml_set | grep ni_dimen | awk -F\" '{print $2}'`
@ nlabels ++
# copy just the labels from the niml dset
3dinfo -labeltable $clust_niml_set | tail -$nlabels | grep -v VALUE_LABEL_DTABLE \
| tr -d \" > temp_labels.txt
MakeColorMap -std ROI_i256 |tail -256 > roi256.1D
# now create a proper SUMA compatible colormap by combining the two files
# index label RGBA
@ nlabels --
rm tempcmap.txt
foreach li (`count -digits 1 1 $nlabels`)
set ind_label = `sed "${li}q;d" temp_labels.txt`
set rgb = `sed "${li}q;d" roi256.1D`
# put them all together (RGB are fractional values, Alpha=1)
# index label R G B A
# 1 electrode_1 0.1 0.4 0.02 1
echo $ind_label $rgb 1 >> tempcmap.txt
end
# create a non-colored copy of the dataset - just nodes and cluster indices
ConvertDset -overwrite -input $clust_niml_set -dset_labels 'R' -o temp_marked_clusters.1D
# make color map used below and updated too
MakeColorMap -usercolutfile tempcmap.txt \
-suma_cmap tempcmap -overwrite >& /dev/null
# -sdset temp_marked_clusters.niml.dset \
####### END of new code for el cluster shading v2.0###########################
# if cluster dataset was not specified, try to find one
if ($clustset == ) then
set clustsets = (3dclusters_r?_is?.nii)
set clustset = $clustsets[0]
endif
afni $NPB -niml -yesplugouts -dset $ct $clustset >& ./afniout.log &
sleep 1
# delete copy of previous surface coordinates and region if it exists
if -e $surfcoords then
mv $surfcoords $surfcoords.old
# mv $surfcoords_i $surfcoords_i.old
endif
# coordinates sent to text file by AFNI with plugout xyz
setenv AFNI_OUTPLUG $surfcoords
# text output from suma driven command with cluster index with surface name
setenv SUMA_OUTPLUG $sumasurf
suma $NPB -DSUMA_AllowDsetReplacement=YES -i $clust_surf -sv $ct >& ./sumaout.log & #####edited for v2.0
DriveSuma $NPB -com surf_cont -view_object_cont y
# We need a way to click on the electrodes in the clinical order and
# find the correspondent center of mass coordinates in clst.1D file.
# The optimal output would be a txt file with four columns, namely:
# Number_of_the_cluster_in_clinical_order coord_x coord_y coord_z
plugout_drive $NPB \
-com 'SWITCH_SESSION A.afni' \
-com 'OPEN_WINDOW A.axialimage geom=600x600+416+44 \
ifrac=0.8 opacity=5' \
-com 'OPEN_WINDOW A.sagittalimage geom=+45+430 \
ifrac=0.8 opacity=5' \
-com "SWITCH_UNDERLAY $ct" \
-com "SWITCH_OVERLAY $clustset" \
-com 'SEE_OVERLAY +' \
-com "SET_OUTPLUG $surfcoords" \
-quit
# suma sends surface object output to a particular file
# and start talking to afni
DriveSuma $NPB \
-com viewer_cont -key t
# set l = `prompt_user -pause
####### START new code for el cluster shading v2.0 (MPBranco 300617)###########################
sleep 2
# update coloring to ROI_i256 instead of IsoSurface coloring (which might be the same anyway)
# and use copy of cluster niml dset for colors that gets updated below
DriveSuma $NPB -com surf_cont -load_dset temp_marked_clusters.1D.dset \
-surf_label $clust_surf
DriveSuma $NPB -com surf_cont -switch_dset temp_marked_clusters.1D.dset
DriveSuma $NPB -com surf_cont -load_cmap tempcmap.niml.cmap
DriveSuma $NPB -com surf_cont -switch_cmap tempcmap -Dim 0.6 \
-switch_cmode Dir -1_only Y
####### END new code for el cluster shading v2.0 (MPBranco 300617)###########################
The electrodes were manually selected using the 3-D clustering image in SUMA. Electrodes were selected individually and in order. SUMA was quit after selection was completed.
This script contains the following commands for electrode selection:
#get the xyz coordinate in the volume
# really only need this for the afni_sphere case
# could be a tiny bit faster without this check most of the time
plugout_drive $NPB \
-com 'GET_DICOM_XYZ' \
-quit
# have suma report its current surface label - which cluster
DriveSuma $NPB -com "get_label"
set clustindex = `tail -2 $sumasurf|head -1` #v2.0. old version=-1 $sumasurf`
set xyzstr = `tail -1 $surfcoords`
# output from plugout is of form "RAI xyz: x y z"
# we can use just part of that
# if we are using the exact location for a sphere, let's mark that here
echo $electrode_i $clustindex $xyzstr[3-5] $afni_sphere >> $surfcoords_i
set clustval = `echo $clustindex | sed 's/roi//' |sed 's/(I,T,B)R=//'|\
sed 's/(I,T,B)numeric=//'`
# make 1/3 bright and add it to the list
# this doesn't change the data in any way here
# much smaller memory leak, 1000 iterations less that 256MB total for suma
set roistr = `ccalc -form "roi%3.3d" $clustval`
# commented lines only useful for checking if roi's have already been recolored
# for coloring with white, gray or other constant color, skip these lines
# use grep to be sure this cluster number is legit and to check status
# don't put any commands beween the grep and status check
# grep $roistr temproilist.txt
# If first time cluster has been identified, recolor to 1/3 brightness
# could make else condition, rebrighten electrode
# if ($status) then
set roirgb = `grep $roistr tempcmap.niml.cmap`
set rgbout = ("1.0" "1.0" "1.0") #old version: `1deval -a "1D:$roirgb[1-3]" -expr a/3`
# change niml file (redirect, then rename rather than in place with "sed -i ..." because of MacOS oddities)
cat tempcmap.niml.cmap | sed "s/$roirgb/$rgbout 1 $roirgb[5] ${roistr}/" > tempcmap2.niml.cmap
mv tempcmap2.niml.cmap tempcmap.niml.cmap
# DriveSuma $NPB -com surf_cont -switch_dset temp_marked_clusters.1D.dset
DriveSuma $NPB -com surf_cont -load_cmap tempcmap.niml.cmap
# echo $roistr >> temproilist.txt
# endif
The third and final step is electrode projection. The log file from the third step does not contain the called commands, the list below has been extracted from the Matlab file runMethod1.m. "Method 1" (Hermes et. al 2010), the subject name "YBK" and the hemisphere "right" were selected in the GUI. The grid settings were then manually created consisting of a label "G", the desired electrodes from the previous selection in step 2 "[1:32]", and grid dimensions "4,8".
The script calls the following commands: (Note that these commands are directly from the MATLAB script, as no .csh file exists for it)
%% NOTES;
% This script uses freesurfer surface with electrode position extracted from
% high res CT 3dclusters (using ctmr scirpt from Dora).
%% 1.1) generate surface to project electrodes to
hemisphere = obj.settings.Hemisphere;
if strcmp(hemisphere, 'Left')
hemi = 'l';
else
hemi = 'r';
end
if exist(['./results/' subject '_balloon_11_03.img'])==0
% if using freesurfer:
get_mask_from_FreeSurfer(subject,... % subject name
'./data/FreeSurfer/t1_class.nii',... % freesurfer class file
'./results/',... % where you want to safe the file
hemi,... % 'l' for left 'r' for right
11,0.3); % settings for smoothing and threshold
%Visualize the surface with afni or mricron
%saved as subject_balloon_11_03, where 11 and 0.3 are the chosen parameters.
end
%% 1.2) Convert DICOM to NIFTI + Coregistration + 3dClustering + electrode selection and sorting
% coregister CT to anatomical MR using Afni and preserving CT resolution.
% extract electrodes clusters using 3D clustering
% extract CM using AFNI-SUMA plug-in.
CM = importdata('./data/3Dclustering/electrode_CM.1D');
%remove repeated electrodes.
[~, index] = unique(CM.data(:,4), 'last');
CM = CM.data(index,[1:4]);
elecCoord = [-CM(:,1:2) CM(:,3)];
elecNum = CM(:,4);
%check for empty rows and put NANs
elecmatrix = zeros(elecNum(end),3); % create empty array
auxk = 2;
elecmatrix(1,:) = elecCoord(1,:);
for k=2:length(elecNum)
if elecNum(k)-elecNum(k-1)~= 1
elecmatrix(elecNum(k-1)+1:elecNum(k)-1,:) = nan;
auxk = elecNum(k);
elecmatrix(auxk,:) = elecCoord(k,:);
auxk = auxk+1;
else
elecmatrix(auxk,:) = elecCoord(k,:);
auxk = auxk +1;
end
end
save([mypath 'CM_electrodes_sorted_all.mat'],'elecmatrix');
%% 4) Tansform coordinates to subject ANAT space:
load([mypath 'CM_electrodes_sorted_all.mat']);
Tmatrix = dlmread('./data/coregistration/CT_highresRAI_res_shft_al_mat.aff12.1D');
Tmatrix2 = dlmread('./data/coregistration/CT_highresRAI_shft.1D');
T = [reshape(Tmatrix',4,3) [0 0 0 1]']';
T2 = [reshape(Tmatrix2',4,3) [0 0 0 1]']';
T3 = T2*T;
coord_al_anatSPM = [];
coord_al_anat = [];
for i = 1:size(elecmatrix,1)
coord = [-elecmatrix(i,1:2) elecmatrix(i,3) 1];
coord_al_anat(i,:) = T3\coord' ; % = inv(T)*coord'
coord_al_anatSPM(i,:) = [-coord_al_anat(i,1:2) coord_al_anat(i,3)];
end
%%%%%%% SPM alignement:
% T = [0.9979 0.0622 0.0154 -13.5301;...
% -0.0629 0.9971 0.0428 -7.2991;...
% -0.0127 -0.0437 0.9990 -19.1397;...
% 0 0 0 1.0000];
%
%coord_al_anatSPM = [];
%
%for i = 1:size(elecmatrix,1)
% coord = [elecmatrix(i,1:3) 1]; %spm mode
% coord_al_anatSPM(i,:) = inv(T)*coord' ;
%end
%%%%%%%%%%%%%%%%%
% check result:
% figure,
% plot3(coord_al_anatSPM(:,1),coord_al_anatSPM(:,2),coord_al_anatSPM(:,3),'.','MarkerSize',20); hold on;
% plot3(elecmatrix(:,1),elecmatrix(:,2),elecmatrix(:,3),'.r','MarkerSize',20); legend('aligned');
elecmatrix = coord_al_anatSPM(:,1:3);
save([mypath 'CM_electrodes_sorted_all_aligned.mat'],'elecmatrix');
%% 5) project electrodes 2 surface
system(['rm ./results/' subject '_singleGrid*']);
load([mypath 'CM_electrodes_sorted_all_aligned.mat']);
% electrodes2surf(subject,localnorm index,do not project electrodes closer than 3 mm to surface)
% electrodes are projected per grid with electrodes2surf.m
% in this example there were 7 grids
% electrodes2surf(
% 1: subject
% 2: number of electrodes local norm for projection (0 = whole grid)
% 3: 0 = project all electrodes, 1 = only project electrodes > 3 mm
% from surface, 2 = only map to closest point (for strips)
% 4: electrode numbers
% 5: (optional) electrode matrix.mat (if not given, SPM_select popup)
% 6: (optional) surface.img (if not given, SPM_select popup)
% 7: (optional) mr.img for same image space with electrode
% positions
% automatically saves:
% a matrix with projected electrode positions
% a nifti image with projected electrodes
% saved as electrodes_onsurface_filenumber_inputnr2
electrodes_path = [mypath 'CM_electrodes_sorted_all_aligned.mat'];
surface_path = [mypath subject '_balloon_11_03.img'];
anatomy_path = './data/FreeSurfer/t1_class.nii';
for g=1:size(obj.settings.Grids,2)
grid = obj.settings.Grids{g};
%find comas:
comas = strfind(grid,',');
gridLabel = grid(1:comas(1)-1);
gridEls = str2num(grid(comas(1)+1:comas(2)-1));
gridSize = str2num(grid(comas(2)+1:end));
if min(gridSize)==1
%strip
parm(1) = 0;
parm(2) = 2;
elseif min(gridSize)==2
%small grid 2xN
parm(1) = 4;
parm(2) = 1;
elseif min(gridSize)>2
%big grids: 3xN, 4xN, 6xN, 8xN
parm(1) = 5;
parm(2) = 1;
else
disp('! WARNING: Grid cannot have dimension 0. Please add grid again.');
%log
str = get(obj.controls.txtLog, 'string');
if length(str)>=obj.settings.NUM_LINES
str = str( (end - (obj.settings.NUM_LINES-1)) :end);
end
set(obj.controls.txtLog, 'string',{str{:},'>! WARNING: Grid cannot have dimension 0. Please add grid again.'});
loggingActions(obj.settings.currdir,3,' >! WARNING: Grid cannot have dimension 0. Please add grid again.');
end
try
[out_els,out_els_ind]=electrodes2surf_FreeSurfer(subject,parm(1),parm(2),gridEls,electrodes_path, surface_path, anatomy_path, mypath);
catch
parm(2) = 2;
[out_els,out_els_ind]=electrodes2surf_FreeSurfer(subject,parm(1),parm(2),gridEls,electrodes_path, surface_path, anatomy_path, mypath);
end
elecmatrix(gridEls,:) = out_els;
end
%save as subject_singleGrid_projectedElectrodes_FreeSurfer_X_parm1_parm2,
%where X is the number of the generated file (1 for the first file with
%parameters X, Y and 2 for second file with same parameters),
%and parm1 and parm2 the 2nd and 3rd of the projection function.
%% 6) combine electrode files into one
% save all projected electrode locaions in a .mat file
save([mypath subject '_projectedElectrodes_FreeSurfer_3dclust.mat'],'elecmatrix');
% make a NIFTI image with all projected electrodes
[output,els,els_ind,outputStruct]=...
position2reslicedImage2(elecmatrix,anatomy_path);
for filenummer=1:100
outputStruct.fname=[mypath subject '_projectedElectrodes_FreeSurfer_3dclust' int2str(filenummer) '.img' ];
if ~exist(outputStruct.fname,'file')>0
disp(['saving ' outputStruct.fname]);
% save the data
spm_write_vol(outputStruct,output);
break
end
end
%% 7) generate cortex to render images:
hemisphere = obj.settings.Hemisphere;
if strcmp(hemisphere, 'Left')
% from freesurfer: in mrdata/.../freesurfer/mri
gen_cortex_click_from_FreeSurfer(anatomy_path,[subject '_L'],0.5,[15 3],'l',mypath);
display_view = [270 0];
% load cortex
load([mypath subject '_L_cortex.mat']);
save([mypath '/projected_electrodes_coord/' subject '_L_cortex.mat'],'cortex');
elseif strcmp(hemisphere, 'Right')
% from freesurfer: in mrdata/.../freesurfer/mri
gen_cortex_click_from_FreeSurfer(anatomy_path,[subject '_R'],0.5,[15 3],'r',mypath);
display_view = [90 0];
% load cortex
load([mypath subject '_R_cortex.mat']);
save([mypath '/projected_electrodes_coord/' subject '_R_cortex.mat'],'cortex');
end
%% 8) plot electrodes on surface
% load electrodes on surface
load([mypath subject '_projectedElectrodes_FreeSurfer_3dclust.mat']);
% save final folder
save([mypath '/projected_electrodes_coord/' subject '_projectedElectrodes_FreeSurfer_3dclust.mat'],'elecmatrix')
ctmr_gauss_plot(cortex,[0 0 0],0);
el_add(elecmatrix,'r',20);
label_add(elecmatrix)
loc_view(display_view(1), display_view(2));
