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p147685 2020-03-30 07:29:01 +02:00
parent 3440e5b6d8
commit 4add96e8bb
2 changed files with 218 additions and 36 deletions
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213
resources/BSM_Class/BSM.m
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@ -5,9 +5,12 @@ classdef BSM<handle
properties %public properties
SPMs={}; %field to contain the full path of all SPM.mat files to be analysed
Acfl %columns in SPM.xX.X to ignore
Type=1; %BSM type 1..4 5: none
Type=4; %BSM type 1..4 5: none %default is option 4
KeepMP = false; %retain Motion paramters
Prefix = 'bs'; %beta series prefix
Clean = true;
end
properties %private properties
properties (Access = private)%private properties
SPM_orig %temporary storage for SPM.mat file
ActiveColumns %store the columns to be analized
U_orig %store the U field of SPM
@ -16,16 +19,34 @@ classdef BSM<handle
BSMToolboxPath%store path to BSMToolbox
SPMPath;%store path to SPM folder
SPMIndexList=[];
MonitorState=false;
end
properties (Dependent) %dependent properties
NumSPMs% number of SPM.mat files to process
end
properties %constants
properties (Constant = true)%constants
BSMMethod={'Traditional BSM Rissman et al', 'Adapted BSM Rissman et al', 'Fast approach (Mumford et al)', 'Adapted fast approach','none'};
end
methods %user callable methods
function Monitor(obj,varargin)
if numel(varargin)>1
id = 'BSM:Monitor:TooManyInputs';
msg= sprintf('Too many inputs given.\n Use: \t obj.Monitor\n\tobj.Monitor(true)\n\tobj.monitor(false)\n');
throw(MException(id,msg))
end
if numel(varargin)==0
obj.MonitorState=xor(obj.MonitorState,true);
else
if ~islogical(varargin{1})
id = 'BSM:Monitor:InputIsNotLogical';
msg= sprintf('Input is not of type logical\n');
throw(MException(id,msg))
end
obj.MonitorState=varargin{1};
end
end
function Calc(obj,varargin)
% obj.calc to apply calculate to all SPM.mat files
% obj.calc(n) to calculated the nth SPM.mat file
@ -97,6 +118,35 @@ classdef BSM<handle
function val=get.NumSPMs(obj)
val=numel(obj.SPMs);
end
function set.SPMPath(obj,~)
SPMFound=which('spm'); %check if SPM in searchpath
if isempty(SPMFound) %SPM not found
error('please add SPM to your path before trying to run BSM');
%to do add a check on spm version
end
obj.SPMPath=fileparts(SPMFound);
end
function set.Clean(obj,varargin)
if isempty(varargin)
%% this option is obsolete
obj.Clean=xor(obj.Clean,true); %togle state
elseif ~islogical(varargin{1})
id = 'BSM:SetClean:InvalidType';
msg= 'Value passed to obj.Clean is not of type logical';
throw(MException(id,msg));
else
obj.Clean=varargin{1};
end
end
function set.Prefix(obj,val)
if ischar(val)
obj.Prefix=val;
else
id='BSM:SetPrefix:InvalidInput';
msg='Input needs to be a char array';
throw(MException(id,msg));
end
end
function set.Type(obj,val)
%check allowed input
if ~isnumeric(val)|| any(~ismember(val,1:5))
@ -155,7 +205,7 @@ classdef BSM<handle
obj.SPMs=val;
end
end
methods %private functions
methods (Access = protected)%private functions
function CoreCalc(obj,idx)
fprintf('working on :%d: %s\n',idx,obj.SPMs{idx});
% how to store the current status of warning and restore curent
@ -168,7 +218,7 @@ classdef BSM<handle
load(SpmFile); %#ok<LOAD>
%% exception block
%NB these exception has not been tested properly by the
if (SPM.xBF.order ~=1 )
if (SPM.xBF.order ~=1 ) %#ok<*NODEF>
%TestBSMClass program
%throw an error. The calling function should properly
%handle the error.
@ -190,7 +240,7 @@ classdef BSM<handle
%% set local variables
SPMOrig = SPM;
UOrig = SPM.Sess(1).U;
[ActCol,PasCol,AllCol]=obj.GetColDef(UOrig);
[ActCol,~,~]=obj.GetColDef(UOrig);
LocalTargetFolder = fullfile(fileparts(SpmFile),'BSM');%RR replace BSM by a obj.BSMDir so user can modify this
%% create directory
mkdir(LocalTargetFolder);
@ -200,15 +250,17 @@ classdef BSM<handle
CurCol=ActCol(c);
OthCol=setdiff(1:length(ActCol),CurCol);
TargetFolderCurCol=fullfile(LocalTargetFolder,sprintf('col_%04d', CurCol));
for e=1:numel(UOrig(CurCol).ons)% loop over events
U=obj.GetU(UOrig,e,c)%build U
% build SPM
% process SPM
% Cleanup
NEvents=numel(UOrig(CurCol).ons);
DirTrialList=cell(NEvents,1);
BetaTrialList=cell(NEvents,1);
for e=1:NEvents% loop over events
U=obj.GetU(UOrig,e,CurCol,OthCol);%build U
DirTrialList{e}=obj.GenSPM(U,SPMOrig,TargetFolderCurCol,e);%build SPM
obj.RunJob(DirTrialList{e});%process SPM
BetaTrialList{e}=spm_select('ExtFPList',DirTrialList{e},'^beta_0001.*.nii$',1);
end% end loop
% pack per event result
% Cleanup
obj.PackBetas(BetaTrialList,LocalTargetFolder,CurCol)%pack per event result
obj.CleanUp(TargetFolderCurCol);
end % end loop act. col
% restore warning status
warning(WarnStat);
@ -217,15 +269,98 @@ classdef BSM<handle
rethrow(ME);
end
end
function U=GetU(obj,UOrig,Event,Col)
U=struct('name',{},'ons', [], 'dur',[], 'P',[], 'dt', [], 'u', [],'pst',[]);
function CleanUp(~,D)
if obj.Clean
try
rmdir(D,'s');
catch ME
disp(ME)
id = 'BSM:Clean:Failed';
msg= 'Cleaning failed';
throw(MException(id,msg));
end
end
end
function PackBetas(obj,P,wd,Col)
FPFout=fullfile(wd,sprintf('%s_%04d.nii',obj.Prefix,Col));
matlabbatch{1}.spm.util.cat.vols = P;
matlabbatch{1}.spm.util.cat.name = FPFout;
matlabbatch{1}.spm.util.cat.dtype = 4;
spm_jobman('run', matlabbatch);
end
function RunJob(~,swd)
%% estimate model:
matlabbatch{1}.spm.stats.fmri_est.spmmat = {fullfile(swd,'SPM.mat')};
matlabbatch{1}.spm.stats.fmri_est.method.Classical = 1;
spm_jobman('run', matlabbatch);
end
function swd=GenSPM(obj,U,SPMOrig,TargetFolderCol,Event)
SPM=SPMOrig;
TargetFolderColTrial=fullfile(TargetFolderCol,sprintf('trial_%04d',Event));
mkdir(TargetFolderColTrial);
SPM.swd = TargetFolderColTrial;
SPM.Sess.U=U;
U=spm_get_ons(SPM,1); % to have SPM autocomplete the U structure
[X,~,Fc]=spm_Volterra(U,SPM.xBF.bf,SPM.xBF.Volterra);
k=SPM.nscan(1);
fMRI_T = SPM.xBF.T;
fMRI_T0 = SPM.xBF.T0;
X = X((0:(k-1))*fMRI_T +fMRI_T0 + 32,:);%@JB what does the +32 do?
%orthogonalize
for k=1:numel(Fc)
X(:,Fc(k).i)=spm_orth(X(:,Fc(k).i));
end
Xname=cell(1,size(X,2));
for k = 1:size(X,2)
Xname{k} = [sprintf('Sn(%i) ',1) SPM.Sess(1).U(k).name{1}];
end
%% reinstate motion parameters
if (obj.KeepMP)&& ~isempty(SPMOrig.Sess(1).C.C)
C = SPMOrig.Sess(1).C.C;
Cname = job.SPM_orig.Sess(1).C.name;
X = cat(2,X,spm_detrend(C));
Xname = cat(2,Xname, Cname(:));
end
%% reinstate baseline column
X(:,end+1) = 1;
Xname = cat(2,Xname,{sprintf('Sn(%i) %s',1,'constant')});
%% monitor
if obj.MonitorState
figure(100);
clf;
imagesc(X);
pause(0.5);
end
%% Rebuild SPM
SPM.xX.X = X;
SPM.xX.iB = size(X,2);
SPM.xX.iC = 1:size(X,2)-1;
SPM.xX.name = Xname;
try
SPM.xX = rmfield(SPM.xX,'W');%remove prewhitening matrix
catch
end
save(fullfile(SPM.swd,'SPM.mat'),'SPM');
swd=SPM.swd;
end
function U=GetU(obj,UOrig,Event,Col,OCol)
U=struct('name',{},'ons', [], 'dur', [],'orth', [], 'P', [], 'dt', [], 'u', [],'pst',[]);
idx=1;
%split out current event as first condition
U(idx).name{1} = sprintf('%s_%d',UOrig(Col).name{1},Event);
U(idx).ons = UOrig(Col).ons(Event);
U(idx).dur = UOrig(Col).dur(Event);
U(idx).orth = UOrig(Col).orth;
U(idx).P = UOrig(Col).P;
U(idx).dt = UOrig(Col).dt;
% u
% pst
%optional add all other events as the next condition
switch obj.Type
case {1,2}
@ -234,16 +369,46 @@ classdef BSM<handle
U(idx).name{1} = sprintf('%s_oe',UOrig(Col).name{1});
U(idx).ons = UOrig(Col).ons(OtherTrials);
U(idx).dur = UOrig(Col).dur(OtherTrials);
U(idx).orth = UOrig(Col).orth;
U(idx).P = UOrig(Col).P;
U(idx).dt = UOrig(Col).dt;
% u
% pst
case {3,4}
otherwise
end
% deal with other conditions
switch obj.Type
case {1,4} %put all other conditions in one column
case {2,3} %keep other conditions each in their own column
otherwise
if ~isempty(OCol)
switch obj.Type
case {1,4} %put all other conditions in one column
idx = idx + 1;
U(idx).name{1} = 'AllOtherConditions';
U(idx).ons = cat(1,UOrig(OCol).ons);
for k = OCol
if numel(UOrig(k).dur)==1
dur=repmat(UOrig(k).dur,size(UOrig(k).ons));
elseif numel(UOrig(k).dur)==numel(UOrig(k).ons)
dur=UOrig(k).dur;
else
id='BSM:GetU:InvalidNumberDuration';
msg=sprintf('%s\n'...
,'Number of durations is neither one nor the number of onsets'...
);
throw(MException(id,msg));
end
U(idx).dur=cat(1,U(idx).dur,dur);
U(idx).orth = UOrig(k).orth;
U(idx).P = UOrig(k).P;
U(idx).dt = UOrig(k).dt;
end
case {2,3} %keep other conditions each in their own column
U=cat(2,U,UOrig(OCol));
otherwise
end
%clear out fields u and pst They will be rebuild when SPM
%is created
[U(:).pst]=deal([]);
[U(:).u]=deal([]);
end
end
function [ActCol,PasCol,AllCol]=GetColDef(obj,U)
@ -255,14 +420,6 @@ classdef BSM<handle
end
ActCol = setdiff(AllCol,PasCol);
end
function set.SPMPath(obj,~)
SPMFound=which('spm'); %check if SPM in searchpath
if isempty(SPMFound) %SPM not found
error('please add SPM to your path before trying to run BSM');
%to do add a check on spm version
end
obj.SPMPath=fileparts(SPMFound);
end
function[val,TF]=MyGetVal(~,selector,List)
TF=strcmpi(selector,List);
if any(TF) %spmpath is set as option

41
resources/BSM_Class/TestBSMClass.m
View File

@ -3,7 +3,7 @@
%
%% create an instance
B=BSM;
%%
%% test initialization
clear B
try
B=BSM('type',3,'Acfl',[],'SPMs'); %#ok<*NASGU> %will create an error
@ -15,7 +15,7 @@ catch ME
rethrow(ME);
end
end
%%
%% initialize properly
clear B
B=BSM('type',1,'Acfl',[],'SPMs',{});
%% set SPMs validity check
@ -34,19 +34,44 @@ catch ME
rethrow(ME)
end
end
B.SPMs=tmp;
%% set Type check
try
B.Type='onzin'; %gives an error
%%
try
B.SPMs={'SPM.mat';'onzin.mat'}; %provides an error if file does not exist
catch ME
if strcmpi(ME.identifier,'BSM:Type:invalid')
if strcmpi(ME.identifier,'BSM:SetSPMs:FileNotFound')
disp('error properly handled')
disp(ME);
else
rethrow(ME)
end
end
B.SPMs=tmp;
%% set Prefix check
try
B.Prefix=""; %gives an error
catch ME
if strcmpi(ME.identifier,'BSM:SetPrefix:InvalidInput')
disp('error properly handled')
disp(ME);
else
rethrow(ME)
end
end
%%
B.Prefix='bs'
%% set Clean check
try
B.Clean=""; %gives an error
catch ME
if strcmpi(ME.identifier,'BSM:SetClean:InvalidType')
disp('error properly handled')
disp(ME);
else
rethrow(ME)
end
end
disp(B.Clean)
B.Clean=true;
%% Check Type set
try
B.Type=0; %gives an error
catch ME