From 469a91a606bc42cd548df77f338e96d25a5792b1 Mon Sep 17 00:00:00 2001
From: Julien Besle <julienbesle@gmail.com>
Date: Thu, 7 Nov 2019 03:52:58 +0200
Subject: [PATCH] (julien) added hrf model hrfCustom.m to add arbitrary HRF
 model using numerical values

---
 .../GLM_v2/newGlmAnalysis/glmAnalysisGUI.m    |  2 +-
 .../Plugin/GLM_v2/newGlmAnalysis/hrfCustom.m  | 63 +++++++++++++++++++
 2 files changed, 64 insertions(+), 1 deletion(-)
 create mode 100644 mrLoadRet/Plugin/GLM_v2/newGlmAnalysis/hrfCustom.m

diff --git a/mrLoadRet/Plugin/GLM_v2/newGlmAnalysis/glmAnalysisGUI.m b/mrLoadRet/Plugin/GLM_v2/newGlmAnalysis/glmAnalysisGUI.m
index c32413da9..972992c87 100644
--- a/mrLoadRet/Plugin/GLM_v2/newGlmAnalysis/glmAnalysisGUI.m
+++ b/mrLoadRet/Plugin/GLM_v2/newGlmAnalysis/glmAnalysisGUI.m
@@ -94,7 +94,7 @@
 askForParams = 1;
 % put group name on top of list to make it the default
 groupNames = putOnTopOfList(params.groupName,viewGet(thisView,'groupNames'));
-hrfModelMenu = putOnTopOfList(params.hrfModel,{'hrfDoubleGamma','hrfFslFlobs','hrfDeconvolution','hrfBoxcar'});
+hrfModelMenu = putOnTopOfList(params.hrfModel,{'hrfDoubleGamma','hrfFslFlobs','hrfDeconvolution','hrfBoxcar','hrfCustom'});
 analysisVolumeMenu = {'Whole volume'};
 if nRois
   analysisVolumeMenu{end+1} = 'Loaded ROI(s)';
diff --git a/mrLoadRet/Plugin/GLM_v2/newGlmAnalysis/hrfCustom.m b/mrLoadRet/Plugin/GLM_v2/newGlmAnalysis/hrfCustom.m
new file mode 100644
index 000000000..8f70a4c87
--- /dev/null
+++ b/mrLoadRet/Plugin/GLM_v2/newGlmAnalysis/hrfCustom.m
@@ -0,0 +1,63 @@
+% hrfDeconvolution.m
+%
+%        $Id$
+%      usage: [params,hrf] = hrfCustom(params, sampleDuration, sampleDelay, defaultParams)
+%         by: julien besle
+%       date: 13/04/2010
+%    purpose: returns the HRF specified as values in the parameters. If a time vector is specified
+%             checks that times correspond to actual TR and acquistion time (sampleDuration and sampleDelay)
+%             otherwise, assumes that HRF sample times correspond to those TR and acquisition times
+%
+function [params,hrf] = hrfCustom(params, sampleDuration,sampleDelay, defaultParams)
+
+if ~any(nargin == [1 2 3 4])% 5])
+  help hrfCustom
+  return
+end
+
+if ieNotDefined('defaultParams'),defaultParams = 0;end
+if ieNotDefined('sampleDelay')
+  sampleDelay=sampleDuration/2;
+end
+
+if ieNotDefined('params')
+  params = struct;
+end
+if fieldIsNotDefined(params,'description')
+  params.description = 'Custom HRF';
+end
+if fieldIsNotDefined(params,'hrf')
+  [~, params.hrf] = hrfDoubleGamma([],sampleDuration,sampleDelay,1);
+  params.hrf = params.hrf';
+end
+if fieldIsNotDefined(params,'hrfTimes')
+  params.hrfTimes = sampleDelay+sampleDuration*(0:length(params.hrf)-1);
+end
+   
+paramsInfo = {...
+    {'description', params.description, 'comment describing the hdr model'},...
+    {'hrf',params.hrf,'values of the the HRF'},...
+    {'hrfTimes',params.hrfTimes,'Times of the HRF samples'},...
+};
+      
+if defaultParams
+  params = mrParamsDefault(paramsInfo);
+else
+  params = mrParamsDialog(paramsInfo, 'Set Custom HRF parameters');
+end
+
+if nargout==1
+   return
+end
+
+%check that the times correspond to 
+if ~isequal(sampleDelay+sampleDuration*(0:length(params.hrf)-1), params.hrfTimes)
+  mrWarnDlg('(hrfCustom) HRF times are not compatible with TR and acquisition time'); 
+  keyoard
+else
+  if size(params.hrf,1)==1
+    hrf = params.hrf';
+  else
+    hrf = params.hrf;
+  end
+end
\ No newline at end of file