modified: TORTOISEV4/CMakeLists.txt

	new file:   src/tools/Combine3DImagesTo4D/Combine3DImagesTo4D.cxx
	new file:   src/tools/CombineDWIs/combine_dwis_with_bmatrix.h
	new file:   src/tools/import_bruker/ImportBruker.cxx
	new file:   src/tools/import_bruker/bruker_anatomical_parser.cxx
	new file:   src/tools/import_bruker/bruker_anatomical_parser.h
	new file:   src/tools/import_bruker/bruker_parser.cxx
	new file:   src/tools/import_bruker/bruker_parser.h
	new file:   src/tools/import_bruker/convert_bruker.cxx
	new file:   src/tools/import_bruker/convert_bruker.h
	new file:   src/tools/import_bruker/convert_bruker_anatomical.cxx
	new file:   src/tools/import_bruker/convert_bruker_anatomical.h
	new file:   src/tools/import_bruker/import_bruker.cxx
	new file:   src/tools/import_bruker/import_bruker_anatomical.cxx

Author: eurotomania

TORTOISEV4/CMakeLists.txt

@@ -8,7 +8,7 @@ SET(USEOPENMP 1)
 
 
 if ( NOT DEFINED USECUDA)
-    SET(USECUDA 1)
+    SET(USECUDA 0)
 endif()
 if ( NOT DEFINED USE_VTK)
     SET(USE_VTK 0)

src/tools/Combine3DImagesTo4D/Combine3DImagesTo4D.cxx

@@ -0,0 +1,28 @@
+#include <string>
+#include <vector>
+#include "defines.h"
+#include "../utilities/write_3D_image_to_4D_file.h"
+
+
+int main(int argc, char *argv[])
+{
+    if(argc < 4)
+    {
+        std::cout<< "Usage: Combine3DImagesTo4D output_nifti_filename nifti1_filename  nifti2_filename  .......... niftiN_filename "<<std::endl;
+        return EXIT_FAILURE;
+    }
+
+    int Nimgs= argc-2;
+
+    for(int i=2;i< argc;i++)
+    {
+        ImageType3D::Pointer img = readImageD<ImageType3D>(argv[i]);
+
+        write_3D_image_to_4D_file<float>(img,argv[1],i-2,Nimgs);
+
+    }
+
+
+    return EXIT_SUCCESS;
+
+}

src/tools/CombineDWIs/combine_dwis_with_bmatrix.h

@@ -0,0 +1,88 @@
+#ifndef __COMBINEDWISWITHBMATRIX_H
+#define __COMBINEDWISWITHBMATRIX_H
+
+
+#include "defines.h"
+#include "../utilities/write_3D_image_to_4D_file.h"
+#include "../utilities/extract_3Dvolume_from_4D.h"
+#include "../utilities/read_bmatrix_file.h"
+#include "../tools/TORTOISEBmatrixToFSLBVecs/tortoise_bmatrix_to_fsl_bvecs.h"
+
+void CombineDWIsWithBMatrix(std::vector<std::string> nii_names, std::string output_name)
+{
+
+    int Nimgs= nii_names.size();
+
+    int tot_Nvols=0;
+    for(int ni=0;ni<Nimgs;ni++)
+    {
+        std::string nii_name = nii_names[ni];
+        itk::NiftiImageIO::Pointer myio = itk::NiftiImageIO::New();
+        myio->SetFileName(nii_name);
+        myio->ReadImageInformation();
+        int Nvols= myio->GetDimensions(3);
+        tot_Nvols+=Nvols;
+    }
+
+    vnl_matrix<double> tot_Bmatrix(tot_Nvols,6);
+    std::cout<<"Total volumes: "<< tot_Nvols<<std::endl;
+
+    int vols_so_far=0;
+    for(int ni=0;ni<Nimgs;ni++)
+    {
+        std::string nii_name = nii_names[ni];
+        ImageType4D::Pointer img = readImageD<ImageType4D>(nii_name) ;
+        int Nvols = img->GetLargestPossibleRegion().GetSize()[3];
+
+        std::string bmtxt_name = nii_name.substr(0,nii_name.rfind(".nii"))+".bmtxt";
+
+        vnl_matrix<double> Bmatrix= read_bmatrix_file(bmtxt_name);
+        tot_Bmatrix.update(Bmatrix,vols_so_far,0);
+
+        for(int v=0;v<Nvols;v++)
+        {
+            ImageType3D::Pointer vol = extract_3D_volume_from_4D(img,v);
+            write_3D_image_to_4D_file<float>(vol,output_name,vols_so_far+v,tot_Nvols);
+        }
+        vols_so_far+=Nvols;
+    }
+
+    std::string bmat_name= output_name.substr(0,output_name.rfind(".nii")) + ".bmtxt";
+    std::string bvals_fname= output_name.substr(0,output_name.rfind(".nii")) + ".bvals";
+    std::string bvecs_fname= output_name.substr(0,output_name.rfind(".nii")) + ".bvecs";
+    std::ofstream outfile(bmat_name);
+    outfile<<tot_Bmatrix;
+    outfile.close();
+
+    vnl_matrix<double> bvecs(3,tot_Nvols);
+    vnl_matrix<double> bvals= tortoise_bmatrix_to_fsl_bvecs(tot_Bmatrix, bvecs);
+
+
+    std::ofstream bvecs_file(bvecs_fname.c_str());
+    for(int i=0;i<3;i++)
+    {
+        for(int j=0;j<tot_Nvols;j++)
+        {
+            if(bvals(0,j)==0)
+                bvecs_file<<"0 ";
+            else
+                bvecs_file<< bvecs(i,j)<< " ";
+        }
+        bvecs_file<<std::endl;
+    }
+    bvecs_file.close();
+
+
+    std::ofstream bvals_file(bvals_fname.c_str());
+
+
+        for(int j=0;j<tot_Nvols;j++)
+        {
+            bvals_file<< bvals(0,j)<< " ";
+        }
+    bvals_file.close();
+
+
+}
+
+#endif