From e823a650c8923d2130f097542d588eb26621e325 Mon Sep 17 00:00:00 2001
From: Tamas Borbath <tamas.borbath@tuebingen.mpg.de>
Date: Wed, 16 Dec 2020 19:07:59 +0100
Subject: [PATCH] Added the export and fitting also of the MC water signals
---
createTestData/fittingLCModelWithTransfer.m | 12 ++++++++++--
createTestData/fitting_all_test_data_profit.m | 16 ++++++++++++++++
2 files changed, 26 insertions(+), 2 deletions(-)
diff --git a/createTestData/fittingLCModelWithTransfer.m b/createTestData/fittingLCModelWithTransfer.m
index 35b8172..d9a3a4b 100644
--- a/createTestData/fittingLCModelWithTransfer.m
+++ b/createTestData/fittingLCModelWithTransfer.m
@@ -1,6 +1,10 @@
function fittingLCModelWithTransfer(LCModelCallerInstance, localFilePath, filenameData, dataPath, ...
- filenameWater, waterPath, currentTEString, copyFiles)
+ filenameWater, waterPath, currentTEString, copyFiles, fitWater)
+if ~exist('fitWater','var')
+ fitWater = false;
+end
+
extensionTable = '.table';
extensionCoord = '.coord';
defaultTE = 'TE24';
@@ -9,7 +13,11 @@ defaultLCModelUser = 'tborbath';
defaultSpectraName = 'XXXX';
defaultWaterRefName = 'YYYY';
controlFilesBase = 'fitsettings_';
-controlFilesBaseSuffix = '_Metabolite.control';
+if fitWater
+ controlFilesBaseSuffix = '_MC_Water.control';
+else %normal case
+ controlFilesBaseSuffix = '_Metabolite.control';
+end
%% file paths setup
controlFilesPathLocal = [localFilePath, 'LCModelConfig/'];
diff --git a/createTestData/fitting_all_test_data_profit.m b/createTestData/fitting_all_test_data_profit.m
index 3564864..f6e58f4 100644
--- a/createTestData/fitting_all_test_data_profit.m
+++ b/createTestData/fitting_all_test_data_profit.m
@@ -97,6 +97,7 @@ for indexSubj = 1:numberOfSubjects
concentrations = cell(numberOfTEs,length(namingSuffixesAve));
concentrations_H2O = cell(numberOfTEs,length(namingSuffixesAve));
+ concentrations_MC_H2O = cell(numberOfTEs,length(namingSuffixesAve));
if ~fitLCModel
FQNs = cell(numberOfTEs,length(namingSuffixesAve));
FQNs2 = cell(numberOfTEs,length(namingSuffixesAve));
@@ -112,6 +113,10 @@ for indexSubj = 1:numberOfSubjects
filenameData = [ subjects{indexSubj}, '_', TE_string namingSuffixAve namingSuffixCoil truncSuffix];
dataExportPathTE = [dataExportPath{indexSubj}, '\\', TE_string, '\\'];
+ load([dataExportPathTE, filenameData, '.mat'],'a')
+ MC_mix =2;
+ filenameData_MC_water = [filenameData, '_MC_water'];
+ a.ExportLcmRaw(dataExportPathTE, filenameData_MC_water, false, 'No', -4.7, 0.05, MC_mix);
if fitLCModel
if use_water_references
try
@@ -120,6 +125,12 @@ for indexSubj = 1:numberOfSubjects
movefile([outputFilesPathLocal filenameData '.*'], dataExportPathTE);
concentrations{indexTE,indexAverageDelete, indexCoilDelete} = ...
importConcentrationLCModelTable([filenameData '.table'],dataExportPathTE, TE_string, 'Met moiety');
+ %MC_water
+% fittingLCModelWithTransfer(LCModelCallerInstance, pathBaseExportFiles, ...
+% filenameData_MC_water, dataExportPathTE, filenameWater, waterPath, TE_string, copyFiles, true);
+% movefile([outputFilesPathLocal filenameData_MC_water '.*'], dataExportPathTE);
+% concentrations_MC_H2O{indexTE,indexAverageDelete, indexCoilDelete} = ...
+% importConcentrationLCModelTable([filenameData_MC_water '.table'],dataExportPathTE, TE_string, 'Met moiety');
catch
concentrations{indexTE,indexAverageDelete, indexCoilDelete} = {};
continue;
@@ -132,6 +143,7 @@ for indexSubj = 1:numberOfSubjects
else %TODO
if use_water_references
fittingProFit(filenameData, dataExportPathTE, filenameWater, waterPath, TEs(indexTE), TR, dataExportPathTE);
+ fitting_MC_water(filenameData_MC_water, dataExportPathTE, TEs(indexTE), TR, dataExportPathTE)
else
fittingProFit(filenameData, dataExportPathTE, [], [], TEs(indexTE), TR, dataExportPathTE);
end
@@ -139,6 +151,8 @@ for indexSubj = 1:numberOfSubjects
plot_ProFit_Metabolites_Fit([filenameData, '_profit.mat'],dataExportPathTE, 'Met', true);
load([dataExportPathTE, filenameData, '_profit_H2O.mat'],'concH2O');
concentrations_H2O{indexTE,indexAverageDelete, indexCoilDelete}=concH2O;
+ load([dataExportPathTE, filenameData_MC_water, '_profit.mat'],'concH2O');
+ concentrations_MC_H2O{indexTE,indexAverageDelete, indexCoilDelete}=concH2O;
end
close all
end
@@ -146,9 +160,11 @@ for indexSubj = 1:numberOfSubjects
end
if fitLCModel
save([dataExportPath{indexSubj}, 'concentrations' truncSuffix '.mat'], 'concentrations');
+ save([dataExportPath{indexSubj}, 'concentrations', truncSuffix '_MC_H2O.mat'], 'concentrations_MC_H2O');
else
save([dataExportPath{indexSubj}, 'concentrations', truncSuffix '_profit.mat'], 'concentrations', 'activeMetabolites', 'FQNs', 'FQNs2');
save([dataExportPath{indexSubj}, 'concentrations', truncSuffix '_H2O_profit.mat'], 'concentrations_H2O');
+ save([dataExportPath{indexSubj}, 'concentrations', truncSuffix '_MC_H2O_profit.mat'], 'concentrations_MC_H2O');
end
end
--
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