Beauchamp:ALICE

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:

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));