initial commit, I'm trying to put together a set of streamlined NODDI scripts...

initial commit, I'm trying to put together a set of streamlined NODDI scripts to ease the use of the package

HABSAgeJustified.txt

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+

HABSNODDI.m

+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