solved by manually modifying
.vcxproj of 6 files :

CppUnit.vcxproj
DCMTK.vcxproj
Eigen.vcxproj
GDCM.vcxproj
ITK.vcxproj
OpenCV.vcxproj
Poco.vcxproj
Qwt.vcxproj
tinyxml.vcxproj
VTK.vcxproj

replace
c:\projets\img\MITK\bin\patch.exe
by
c:\projets\img\MITK\bin\patch.exe --binary

-- 
Bien cordialement,
Lotfi

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