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| ##### About | ||
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| dcm2nii is a designed to convert neuroimaging data from the NIfTI format to the DICOM format. For details and compiled versions visit the [NITRC wiki](http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage) | ||
| This is a collection of Matlab scripts that can help with using [SPM](http://www.fil.ion.ucl.ac.uk/spm/software/spm12/) | ||
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| ##### Versions | ||
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| 2-Feb-2015 | ||
| - Support for Visual Studio | ||
| - Remove dependency on zlib (now uses miniz) | ||
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| 1-Jan-2015 | ||
| - Images separated based on TE (fieldmaps) | ||
| - Support for JPEG2000 using OpenJPEG or Jasper libraries | ||
| - Support for JPEG using NanoJPEG library | ||
| - Support for lossless JPEG using custom library | ||
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| 24-Nov-2014 | ||
| - Support for CT scans with gantry tilt and varying distance between slices | ||
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| 11-Oct-2014 | ||
| - Initial public release | ||
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| Building command line version: | ||
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| This requires a C compiler. With a terminal, change directory to the 'conosle' folder and run the following: | ||
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| ##### DEFAULT BUILD | ||
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| - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix | ||
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| ##### ZLIB BUILD | ||
| If we have zlib, we can use it (-lz) and disable [miniz](https://code.google.com/p/miniz/) (-myDisableMiniZ) | ||
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| - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix -lz -DmyDisableMiniZ | ||
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| ##### MINGW BUILD | ||
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| If you use the (osbsolete) compiler MinGW on Windows you will want to include the rare libgcc libraries with your executable so others can use it. Here I also demonstrate the optional "-DmyDisableZLib" to remove zip support. | ||
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| - g++ -O3 -s -DmyDisableOpenJPEG -DmyDisableZLib -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix -static-libgcc | ||
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| ##### JPEG2000 BUILD | ||
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| If you want to build this with JPEG2000 decompression support using OpenJPEG. You will need to have the OpenJPEG 2.1 libraries installed (https://code.google.com/p/openjpeg/wiki/Installation). I suggest building static libraries... | ||
| svn checkout http://openjpeg.googlecode.com/svn/trunk/ openjpeg-read-only | ||
| cmake -DBUILD_SHARED_LIBS:bool=off . | ||
| make | ||
| sudo make install | ||
| You should then be able to run then run: | ||
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| - g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix -lopenjp2 | ||
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| But in my experience this works best if you explicitly tell the software how to find the libraries, so your compile will probably look like one of these two options: | ||
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| - g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix -I/usr/local/include /usr/local/lib/libopenjp2.a | ||
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| - g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix -I/usr/local/lib /usr/local/lib/libopenjp2.a | ||
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| If you want to build this with JPEG2000 decompression support using Jasper: You will need to have the Jasper (http://www.ece.uvic.ca/~frodo/jasper/) and libjpeg (http://www.ijg.org) libraries installed which for Linux users may be as easy as running 'sudo apt-get install libjasper-dev' (otherwise, see http://www.ece.uvic.ca/~frodo/jasper/#doc). You can then run: | ||
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| - g++ -O3 -DmyDisableOpenJPEG -DmyEnableJasper -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -s -o dcm2niix -ljasper -ljpeg | ||
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| ##### VISUAL STUDIO BUILD | ||
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| You should be able to click on the Visual Studio icons to open and build this code. Here are links for for building with [Windows XP support](http://blogs.msdn.com/b/vcblog/archive/2012/10/08/windows-xp-targeting-with-c-in-visual-studio-2012.aspx) and [64-bit support](https://msdn.microsoft.com/en-us/library/9yb4317s.aspx). | ||
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| ##### OSX BUILD WITH BOTH 32 AND 64-BIT SUPPORT | ||
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| Building command line version universal binary from OSX 64 bit system: | ||
| This requires a C compiler. With a terminal, change directory to the 'conosle' folder and run the following: | ||
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| - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -arch i386 -o dcm2niix32 | ||
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| - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix64 | ||
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| - lipo -create dcm2niix32 dcm2niix64 -o dcm2niix | ||
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| To validate that the resulting executable supports both architectures type | ||
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| - file ./dcm2niix | ||
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| ##### OSX GRAPHICAL INTERFACE BUILD | ||
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| Building OSX graphical user interface using XCode: | ||
| Copy contents of "console" folder to /xcode/dcm2/core | ||
| Open and compile "dcm2.xcodeproj" with XCode 4.6 or later | ||
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| ##### THE QT AND wxWIDGETS GUIs ARE NOT YET SUPPORT - FOLLOWING LINES FOR FUTURE VERSIONS | ||
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| Building QT graphical user interface: | ||
| Open "dcm2.pro" with QTCreator. This should work on OSX and Linux. On Windows the printf information is not redirected to the user interface | ||
| If compile gives you grief look at the .pro file which has notes for different operating systems. | ||
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| Building using wxWidgets | ||
| wxWdigets makefiles are pretty complex and specific for your operating system. For simplicity, we will build the "clipboard" example that comes with wxwidgets and then substitute our own code. The process goes something like this. | ||
| a.) Install wxwdigets | ||
| b.) successfully "make" the samples/clipboard program | ||
| c.) DELETE console/makefile. WE DO NOT WANT TO OVERWRITE the WX MAKEFILE | ||
| d.) with the exception of "makefile", copy the contents of console to /samples/clipboard | ||
| e.) overwrite the original /samples/clipboard.cpp with the dcm2niix file of the same name | ||
| f.) Older XCodes have problems with .cpp files, whereas wxWidgets's makefiles do not compile with "-x cpp". So the core files are called '.c' but we will rename them to .cpp for wxWidgets: | ||
| rename 's/\.c$/\.cpp/' * | ||
| g.) edit the /samples/clipboard makefile: Add "nii_dicom.o nifti1_io_core.o nii_ortho.o nii_dicom_batch.o \" to CLIPBOARD_OBJECTS: | ||
| CLIPBOARD_OBJECTS = \ | ||
| nii_dicom.o nifti1_io_core.o nii_ortho.o nii_dicom_batch.o \ | ||
| $(__clipboard___win32rc) \ | ||
| $(__clipboard_os2_lib_res) \ | ||
| clipboard_clipboard.o | ||
| h.) edit the /samples/clipboard makefile: With wxWidgets we will capture std::cout comments, not printf, so we need to add "-DDmyUseCOut" to CXXFLAGS: | ||
| CXXFLAGS = -DmyUseCOut -DWX_PRECOMP .... | ||
| i.) For a full refresh | ||
| rm clipboard | ||
| rm *.o | ||
| make | ||
| First Header | Second Header | ||
| ------------- | ------------- | ||
| Content Cell | Content Cell | ||
| Content Cell | Content Cell |