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William Stonewall Monroe
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function HABSNODDI(i)
addpath(genpath('/data/project/dti/For_William/matlab/NODDI_toolbox_v1.0'));
%readHABSlist
%PatientNumber=HABSlist;
readNotDoneHabs
PatientNumber=notdoneHABSODI;
% i=1;
% for i=1:length(PatientNumber)%floor((4*length(PatientNumber))/5):length(PatientNumber)
% % while(exist(char(strcat('/data/project/lahtilab/NK/freewater/HC/',PatientNumber(i),'.NODDIroi.mat')),'file') == 2)
% % i++;
% % end
% % 3175 has no DWI and 3116 and 3367 and 3372
% [bVal, bGradX, bGradY, bGradZ] = textread(char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.BVEC.r2.txt')),'%f %f %f %f');
% lengthB = length(bGradX);
% %
% fileID = fopen(char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.r2.bval')),'w');
% %
% formatSpec = '%f ';
% %
% for j=1:lengthB
% fprintf(fileID,formatSpec,bVal(j));
% end
% fclose(fileID);
% %
% clear fileID
% %
% fileID = fopen(char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.r2.bvec')),'w');
% %
% formatSpec = '%f ';
% %
% for j=1:lengthB
% fprintf(fileID,formatSpec,bGradX(j));
% end
% %
% fprintf(fileID,'\n');
% %
% for j=1:lengthB
% fprintf(fileID,formatSpec,bGradY(j));
% end
% %
% fprintf(fileID,'\n');
% %
% for j=1:lengthB
% fprintf(fileID,formatSpec,bGradZ(j));
% end
% fclose(fileID);
% % /data/project/dti/For_William/harvard/dwi
% clear fileID
% end
CreateROI(char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.DWI.r.med.refit.nii')),char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.Brainstem.nii')),char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.NODDIroi.mat')));
%CreateROI('/data/project/dti/For_William/rotateDWIv2/finalrotatedDWIv2/3111.DWI.rotat.med.nii','/data/project/dti/For_William/warpedROI/3111.BrainstemMask.nii','NODDIroi1.mat')
protocol = FSL2Protocol(char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.r2.bval')),char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.r2.bvec')));
noddi = MakeModel('WatsonSHStickTortIsoV_B0');
batch_fitting(char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.NODDIroi.mat')),protocol,noddi,char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.FittedParams.mat')),16);
SaveParamsAsNIfTI(char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.FittedParams.mat')),char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.NODDIroi.mat')),char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.Brainstem.nii')),char(strcat('/data/project/dti/For_William/harvard/dwi/',PatientNumber(i),'.noddi')))
end