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Bugfix: Epileptogenicity and delay display
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@ftadel
ftadel committed Mar 10, 2020
1 parent 76779d7 commit 32cc924
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Showing 5 changed files with 55 additions and 29 deletions.
1 change: 1 addition & 0 deletions toolbox/core/bst_colormaps.m
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Expand Up @@ -142,6 +142,7 @@
sColormap.CMap = cmap_viridis(DEFAULT_CMAP_SIZE);
sColormap.isAbsoluteValues = 0;
sColormap.MaxMode = 'global';
sColormap.isRealMin = 1;
% Time-frequency maps
case 'timefreq'
sColormap.Name = 'cmap_magma';
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6 changes: 5 additions & 1 deletion toolbox/gui/panel_surface.m
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Expand Up @@ -1561,7 +1561,11 @@ function UpdateSurfaceProperties()
% === CHECKS ===
% If min/max values for this file were not computed yet
if isempty(TessInfo(iTess).DataMinMax)
TessInfo(iTess).DataMinMax = bst_memory('GetResultsMaximum', iDS, iResult);
if isequal(GlobalData.DataSet(iDS).Results(iResult).ColormapType, 'time')
TessInfo(iTess).DataMinMax = GlobalData.DataSet(iDS).Results(iResult).Time;
else
TessInfo(iTess).DataMinMax = bst_memory('GetResultsMaximum', iDS, iResult);
end
end
% Reset Overlay cube
TessInfo(iTess).OverlayCube = [];
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19 changes: 12 additions & 7 deletions toolbox/io/import_sources.m
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Expand Up @@ -176,6 +176,7 @@
%% ===== READ SOURCE FILES =====
sMri = [];
maps = cell(1, length(SourceFiles));
SPM = cell(1, length(SourceFiles));
% Loop on each input file
for iFile = 1:length(SourceFiles)
% === GET FILE TYPE ===
Expand Down Expand Up @@ -241,27 +242,31 @@
end
break;
end
% Load SPM results
if isStat
% Load SPM.mat
SpmMat = load(fullfile(fPath, 'SPM.mat'));
SPM{iFile} = SpmMat.SPM;
% Add sorted T values in the file if importing from a volume (not keeping the full distribution otherwise)
if ~isempty(grid)
SPM{iFile}.SortedT = sort(sMriSrc.Cube(:));
end
end
end
% Concatenate in time all the selected files
map = cat(2, maps{:});

% === STATISTICAL THRESHOLD (SPM) ===
if isStat
% Load SPM.mat
SpmMat = load(fullfile(fPath, 'SPM.mat'));
% New stat/results structure
ResultsMat = db_template('statmat');
ResultsMat.tmap = map;
ResultsMat.pmap = [];
ResultsMat.df = [];
ResultsMat.SPM = SpmMat.SPM;
ResultsMat.SPM = SPM;
ResultsMat.Correction = 'no';
ResultsMat.Type = 'results';
FileType = 'presults';
% Add sorted T values in the file if importing from a volume (not keeping the full distribution otherwise)
if ~isempty(grid)
ResultsMat.SPM.SortedT = sort(sMriSrc.Cube(:));
end
% Time vector
if isempty(TimeVector) || (length(TimeVector) ~= size(ResultsMat.tmap,2))
ResultsMat.Time = 0:(size(map,2)-1);
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8 changes: 3 additions & 5 deletions toolbox/process/functions/process_epileptogenicity.m
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Expand Up @@ -145,6 +145,8 @@
sMri = in_mri_bst(sSubject.Anatomy(sSubject.iAnatomy).FileName);

% ===== EXPORT INPUT FILES =====
% Empty temporary folder
gui_brainstorm('EmptyTempFolder');
% Work in Brainstorm's temporary folder
workDir = bst_fullfile(bst_get('BrainstormTmpDir'), 'ImaGIN_epileptogenicity');
% Make sure Matlab is not currently in the work directory
Expand Down Expand Up @@ -364,7 +366,7 @@
% File comment = File name
[tmp, Comment] = bst_fileparts(listFiles(i).name);
% Import file
tmpFile = import_sources(iStudy, [], bst_fullfile(workDir, listFiles(i).name), [], fileFormat, Comment, 's', [fileLatency(1), fileLatency(end)]);
tmpFile = import_sources(iStudy, [], bst_fullfile(workDir, listFiles(i).name), [], fileFormat, Comment, 's', [min(fileLatency), max(fileLatency)]);
% Add history field
tmpFile = bst_history('add', tmpFile, 'epilepto', strHistory);
end
Expand Down Expand Up @@ -437,7 +439,3 @@
end
end





50 changes: 34 additions & 16 deletions toolbox/process/functions/process_extract_pthresh.m
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Expand Up @@ -246,7 +246,7 @@
OutputFiles{1} = DataFile;
end


%% ===== APPLY THRESHOLD =====
function [threshmap, tThreshUnder, tThreshOver] = Compute(StatMat, StatThreshOptions)
% If options not provided, read them from the interface
Expand Down Expand Up @@ -288,22 +288,18 @@
warning('SPM must be in the Matlab path to compute the statistical thresold for this file.');
pmask = ones(size(StatMat.tmap));
else
% Compute threshold for statistical map
df = [StatMat.SPM.xCon(1).eidf, StatMat.SPM.xX.erdf];
S = StatMat.SPM.xVol.S; %-search Volume {voxels}
R = StatMat.SPM.xVol.R; %-search Volume {resels}
% Correction
switch (StatThreshOptions.Correction)
% Note: always one-sided t-test, really the case?
case {'none', 'no'}
tThreshOver = spm_u(StatThreshOptions.pThreshold, df, 'T');
case 'bonferroni'
tThreshOver = spm_uc_Bonf(StatThreshOptions.pThreshold, df, 'T', S, 1);
case 'fdr'
tThreshOver = spm_uc(StatThreshOptions.pThreshold, df, 'T', R, 1, S);
% Threshold each time point independently
if iscell(StatMat.SPM)
pmask = false(size(StatMat.tmap));
for iTime = 1:size(StatMat.tmap, 2)
tThreshOver = GetSpmThreshold(StatMat.SPM{iTime}, StatThreshOptions.Correction, StatThreshOptions.pThreshold);
pmask(:,iTime) = (StatMat.tmap(:,iTime) >= tThreshOver);
end
% Threshold all the time points in the same way
else
tThreshOver = GetSpmThreshold(StatMat.SPM, StatThreshOptions.Correction, StatThreshOptions.pThreshold);
pmask = (StatMat.tmap >= tThreshOver);
end
% Activated voxels
pmask = (StatMat.tmap >= tThreshOver);
tThreshUnder = [];
end
else
Expand Down Expand Up @@ -400,3 +396,25 @@
iMaxUnder = [];
end
end


%% ===== COMPUTE SPM THRESHOLD =====
function tThreshOver = GetSpmThreshold(SPM, Method, pThreshold)
% Compute threshold for statistical map
df = [SPM.xCon(1).eidf, SPM.xX.erdf];
S = SPM.xVol.S; %-search Volume {voxels}
R = SPM.xVol.R; %-search Volume {resels}
% Correction
switch (Method)
% Note: always one-sided t-test, really the case?
case {'none', 'no'}
tThreshOver = spm_u(pThreshold, df, 'T');
case 'bonferroni'
tThreshOver = spm_uc_Bonf(pThreshold, df, 'T', S, 1);
case 'fdr'
tThreshOver = spm_uc(pThreshold, df, 'T', R, 1, S);
end
end



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