dcm2niix, DICOMRead3 addition (freesurfer#888)

* 1. check in package dcm2niix
2. add DICOMRead3/niiRead3 to convert dicom using dcm2niix
3. fix dcmGetDWIParams() to use stricmp() to compare the Manufacturer tag

* set TI to -1 when there is no TI in dicom file for MGH_FREESURFER

* remove unused codes

Co-authored-by: Yujing Huang <[email protected]>

include/DICOMRead.h

@@ -27,6 +27,9 @@
 #include "dicom_objects.h"
 #include "condition.h"
 
+#include "nii_dicom.h"
+#include "nii_dicom_batch.h"
+
 #define NUMBEROFTAGS 24
 #define SHORTSIZE 16
 #ifndef INTSIZE
@@ -59,6 +62,7 @@ typedef unsigned short int BOOL;
 char *SDCMStatusFile = 0;
 char *SDCMListFile = 0;
 int  UseDICOMRead2 = 1; // use new dicom reader by default
+int  UseDICOMRead3 = 0;
 /* These variables allow the user to change the first tag checked to
    get the slice thickness.  This is needed with siemens mag res
    angiogram (MRAs) */
@@ -69,6 +73,7 @@ int AutoSliceResElTag = 0; // automatically determine which tag to use based on
 extern char *SDCMStatusFile;
 extern char *SDCMListFile;
 extern int  UseDICOMRead2;
+extern int  UseDICOMRead3;
 extern long SliceResElTag1;
 extern long SliceResElTag2;
 extern int AutoSliceResElTag;
@@ -286,6 +291,7 @@ int CompareDCMFileInfo(const void *a, const void *b);
 int DCMCountFrames(DICOMInfo **dcmfi_list, int nlist);
 int DCMSliceDir(DICOMInfo **dcmfi_list, int nlist);
 MRI *DICOMRead2(const char *dcmfile, int LoadVolume);
+MRIFSSTRUCT *DICOMRead3(const char *dcmfile, int LoadVolume);
 
 DCM_ELEMENT *GetElementFromFile(const char *dicomfile, long grpid, long elid);
 int AllocElementData(DCM_ELEMENT *e);

mri_convert/CMakeLists.txt

@@ -3,7 +3,7 @@ project(mri_convert)
 # ATH: temporarily turning off this warning
 add_compile_options(-Wno-self-assign)
 
-include_directories(${FS_INCLUDE_DIRS} ${CMAKE_SOURCE_DIR}/packages/dicom)
+include_directories(${FS_INCLUDE_DIRS} ${CMAKE_SOURCE_DIR}/packages/dicom ${CMAKE_SOURCE_DIR}/packages/dcm2niix)
 
 add_executable(mri_convert mri_convert.cpp)
 add_help(mri_convert mri_convert.help.xml)

mri_convert/mri_convert.cpp

@@ -1141,6 +1141,10 @@ int main(int argc, char *argv[])
       forced_in_type = string_to_type(in_type_string);
       force_in_type_flag = TRUE;
     }
+    else if (strcmp(argv[i], "-dicomread3") == 0)
+    {
+      UseDICOMRead3 = 1;
+    }
     else if(strcmp(argv[i], "-dicomread2") == 0)
     {
       UseDICOMRead2 = 1;

mri_otl/CMakeLists.txt

@@ -1,6 +1,6 @@
 project(mri_otl)
 
-include_directories(${FS_INCLUDE_DIRS} ${CMAKE_SOURCE_DIR}/packages/dicom)
+include_directories(${FS_INCLUDE_DIRS} ${CMAKE_SOURCE_DIR}/packages/dicom ${CMAKE_SOURCE_DIR}/packages/dcm2niix)
 
 add_executable(list_otl_labels list_otl_labels.cpp)
 target_link_libraries(list_otl_labels utils)

mri_parse_sdcmdir/CMakeLists.txt

@@ -1,6 +1,6 @@
 project(mri_parse_sdcmdir)
 
-include_directories(${FS_INCLUDE_DIRS} ${CMAKE_SOURCE_DIR}/packages/dicom)
+include_directories(${FS_INCLUDE_DIRS} ${CMAKE_SOURCE_DIR}/packages/dicom ${CMAKE_SOURCE_DIR}/packages/dcm2niix)
 
 add_executable(mri_parse_sdcmdir mri_parse_sdcmdir.cpp)
 target_link_libraries(mri_parse_sdcmdir utils)

mri_probedicom/CMakeLists.txt

@@ -6,6 +6,7 @@ if(OPENGL_FOUND)
     ${FS_INCLUDE_DIRS}
     ${CMAKE_SOURCE_DIR}/packages/dicom
     ${CMAKE_SOURCE_DIR}/packages/glut
+    ${CMAKE_SOURCE_DIR}/packages/dcm2niix
     ${X11_INCLUDE_DIR}
   )
 

mri_watershed/CMakeLists.txt

@@ -1,6 +1,6 @@
 project(mri_watershed)
 
-include_directories(${FS_INCLUDE_DIRS} ${CMAKE_SOURCE_DIR}/packages/dicom)
+include_directories(${FS_INCLUDE_DIRS} ${CMAKE_SOURCE_DIR}/packages/dicom ${CMAKE_SOURCE_DIR}/packages/dcm2niix)
 
 add_executable(mri_watershed mri_watershed.cpp)
 add_help(mri_watershed mri_watershed.help.xml)

packages/CMakeLists.txt

@@ -13,6 +13,7 @@ add_subdirectories(
   xml2
   minc
   dicom
+  dcm2niix
   cephes
   netcdf
   tetgen

packages/dcm2niix/CMakeLists.txt

@@ -0,0 +1,233 @@
+cmake_minimum_required(VERSION 2.8.11)
+
+project(dcm2niix)
+
+# Option Choose whether to use static runtime
+include(ucm.cmake)
+option(USE_STATIC_RUNTIME "Use static runtime" ON)
+if(USE_STATIC_RUNTIME)
+    ucm_set_runtime(STATIC)
+else()
+    ucm_set_runtime(DYNAMIC)
+endif()
+
+# Basic CMake build settings
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE "Release" CACHE STRING
+        "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." FORCE)
+    set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS  "Debug;Release;RelWithDebInfo;MinSizeRel")
+endif()
+
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
+    # using Clang
+    add_definitions(-fno-caret-diagnostics)
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-dead_strip")
+elseif(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+    # using GCC
+    if(NOT (${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 7.1.0))
+        add_definitions(-Wno-format-overflow)    # available since GCC 7.1.0
+    endif()
+    if(NOT (${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.5.0))
+        add_definitions(-Wno-unused-result)    # available since GCC 4.5.0
+    endif()
+    if(NOT (${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.8.0))
+        add_definitions(-fno-diagnostics-show-caret)    # available since GCC 4.8.0
+    endif()
+elseif(MSVC)
+    # using Visual Studio C++
+    add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4018")   # '<': signed/unsigned mismatch
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4068")   # unknown pragma
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4101")   # unreferenced local variable
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4244")   # 'initializing': conversion from 'double' to 'int', possible loss of data
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267")   # 'initializing': conversion from 'size_t' to 'int', possible loss of data
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4305")   # 'argument': truncation from 'double' to 'float'
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4308")   # negative integral constant converted to unsigned type
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4334")   # '<<': result of 32-bit shift implicitly converted to 64 bits
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4800")   # 'uint32_t' : forcing value to bool 'true' or 'false'
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4819")   # The file contains a character that cannot be represented in the current code page
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4996")   # 'access': The POSIX name for this item is deprecated
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /STACK:8388608")  # set "Stack Reserve Size" to 8MB (default value is 1MB)
+endif()
+
+# Compiler dependent flags
+include (CheckCXXCompilerFlag)
+if(UNIX)
+    check_cxx_compiler_flag(-march=armv8-a+crc ARM_CRC)
+    if(ARM_CRC)
+        # wrong answer for Apple Silicon: check_cxx_compiler_flag(-msse2 HAS_SSE2)
+    else()
+	    check_cxx_compiler_flag(-msse2 HAS_SSE2)
+	    if(HAS_SSE2)
+	        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse2 -mfpmath=sse")
+	    endif()
+	endif()
+endif()
+
+set(PROGRAMS dcm2niix)
+
+set(DCM2NIIX_SRCS
+    main_console.cpp
+    nii_dicom.cpp
+    jpg_0XC3.cpp
+    ujpeg.cpp
+    nifti1_io_core.cpp
+    nii_foreign.cpp
+    nii_ortho.cpp
+    nii_dicom_batch.cpp)
+
+option(USE_JPEGLS "Build with JPEG-LS support using CharLS" OFF)
+if(USE_JPEGLS)
+    add_definitions(-DmyEnableJPEGLS)
+    if(MSVC)
+        add_definitions(-DCHARLS_STATIC)
+    endif()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
+
+    set(CHARLS_SRCS
+        charls/jpegls.cpp
+        charls/jpegmarkersegment.cpp
+        charls/interface.cpp
+        charls/jpegstreamwriter.cpp
+        charls/jpegstreamreader.cpp)
+    add_executable(dcm2niix ${DCM2NIIX_SRCS} ${CHARLS_SRCS})
+else()
+    add_executable(dcm2niix ${DCM2NIIX_SRCS})
+endif()
+
+set(ZLIB_IMPLEMENTATION "Miniz" CACHE STRING "Choose zlib implementation.")
+set_property(CACHE ZLIB_IMPLEMENTATION PROPERTY STRINGS  "Miniz;System;Custom")
+if(NOT ${ZLIB_IMPLEMENTATION} STREQUAL "Miniz")
+    if(NOT ${ZLIB_IMPLEMENTATION} STREQUAL "System")
+        set(ZLIB_ROOT ${ZLIB_ROOT} CACHE PATH "Specify custom zlib root directory.")
+        if(NOT ZLIB_ROOT)
+            message(FATAL_ERROR "ZLIB_ROOT needs to be set to locate custom zlib!")
+        endif()
+    endif()
+    find_package(ZLIB REQUIRED)
+    add_definitions(-DmyDisableMiniZ)
+    target_include_directories(dcm2niix PRIVATE ${ZLIB_INCLUDE_DIRS})
+    target_link_libraries(dcm2niix ${ZLIB_LIBRARIES})
+endif()
+
+option(USE_TURBOJPEG "Use TurboJPEG to decode classic JPEG" OFF)
+if(USE_TURBOJPEG)
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(TURBOJPEG REQUIRED libturbojpeg)
+    add_definitions(-DmyTurboJPEG)
+    target_include_directories(dcm2niix PRIVATE ${TURBOJPEG_INCLUDEDIR})
+    target_link_libraries(dcm2niix ${TURBOJPEG_LIBRARIES})
+endif()
+
+option(USE_JASPER "Build with JPEG2000 support using Jasper" OFF)
+if(USE_JASPER)
+    find_package(Jasper REQUIRED)
+    add_definitions(-DmyEnableJasper)
+    target_include_directories(dcm2niix PRIVATE ${JASPER_INCLUDE_DIR})
+    target_link_libraries(dcm2niix ${JASPER_LIBRARIES})
+endif()
+
+option(USE_OPENJPEG "Build with JPEG2000 support using OpenJPEG" OFF)
+if(USE_OPENJPEG)
+    set(OpenJPEG_DIR "${OpenJPEG_DIR}" CACHE PATH "Path to OpenJPEG configuration file" FORCE)
+
+    find_package(OpenJPEG REQUIRED)
+
+    if(WIN32)
+        if(BUILD_SHARED_LIBS)
+            add_definitions(-DOPJ_EXPORTS)
+        else()
+            add_definitions(-DOPJ_STATIC)
+        endif()
+    endif()
+
+    target_include_directories(dcm2niix PRIVATE ${OPENJPEG_INCLUDE_DIRS})
+    target_link_libraries(dcm2niix ${OPENJPEG_LIBRARIES})
+else ()
+    add_definitions(-DmyDisableOpenJPEG)
+endif()
+
+option(BATCH_VERSION "Build dcm2niibatch for multiple conversions" OFF)
+if(BATCH_VERSION)
+    set(DCM2NIIBATCH_SRCS
+        main_console_batch.cpp
+        nii_dicom.cpp
+        jpg_0XC3.cpp
+        ujpeg.cpp
+        nifti1_io_core.cpp
+        nii_foreign.cpp
+        nii_ortho.cpp
+        nii_dicom_batch.cpp)
+
+    if(USE_JPEGLS)
+        add_executable(dcm2niibatch ${DCM2NIIBATCH_SRCS} ${CHARLS_SRCS})
+    else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+        add_executable(dcm2niibatch ${DCM2NIIBATCH_SRCS})
+    endif()
+
+    set(YAML-CPP_DIR ${YAML-CPP_DIR} CACHE PATH "Path to yaml-cpp configuration file" FORCE)
+
+    find_package(YAML-CPP REQUIRED)
+    target_include_directories(dcm2niibatch PRIVATE ${YAML_CPP_INCLUDE_DIR})
+    target_link_libraries(dcm2niibatch ${YAML_CPP_LIBRARIES})
+
+    if(ZLIB_FOUND)
+        target_include_directories(dcm2niibatch PRIVATE ${ZLIB_INCLUDE_DIRS})
+        target_link_libraries(dcm2niibatch ${ZLIB_LIBRARIES})
+    endif()
+
+    if(TURBOJPEG_FOUND)
+        target_include_directories(dcm2niibatch PRIVATE ${TURBOJPEG_INCLUDEDIR})
+        target_link_libraries(dcm2niibatch ${TURBOJPEG_LIBRARIES})
+    endif()
+
+    if(JASPER_FOUND)
+        target_include_directories(dcm2niibatch PRIVATE ${JASPER_INCLUDE_DIR})
+        target_link_libraries(dcm2niibatch ${JASPER_LIBRARIES})
+    endif()
+
+    if(OPENJPEG_FOUND)
+        target_include_directories(dcm2niibatch PRIVATE ${OPENJPEG_INCLUDE_DIRS})
+        target_link_libraries(dcm2niibatch ${OPENJPEG_LIBRARIES})
+    endif()
+
+    list(APPEND PROGRAMS dcm2niibatch)
+endif()
+
+
+if(APPLE)
+    message("--   Adding Apple plist")
+    set_target_properties(dcm2niix PROPERTIES LINK_FLAGS "-Wl,-sectcreate,__TEXT,__info_plist,${CMAKE_SOURCE_DIR}/Info.plist")
+    #Apple notarization requires a Info.plist
+    # For .app bundles, the Info.plist is a separate file, for executables it is appended as a section
+    #you can check that the Info.plist section has been inserted with either of these commands
+    # otool -l ./dcm2niix | grep info_plist -B1 -A10
+    # launchctl plist ./dcm2niix
+endif()
+
+### start of addition for FREESURFER
+# we should not need this if we use target_compile_definitions()
+#target_link_libraries(dcm2niix nifti ${ZLIB_LIBRARIES})
+
+set(LIBRARY dcm2niixfs)
+add_library(dcm2niixfs STATIC
+    dcm2fsWrapper.cpp
+    nii_dicom.cpp
+    jpg_0XC3.cpp
+    ujpeg.cpp
+    nifti1_io_core.cpp
+    nii_foreign.cpp
+    nii_ortho.cpp
+    nii_dicom_batch.cpp)
+target_compile_definitions(dcm2niixfs PUBLIC -DMGH_FREESURFER -DUSING_MGH_NIFTI_IO)
+
+set(DCM2NIIXFSEXE dcm2niixfsexe)
+add_executable(${DCM2NIIXFSEXE} dcm2fsmain.cpp)
+target_link_libraries(${DCM2NIIXFSEXE} dcm2niixfs nifti ${ZLIB_LIBRARIES})
+### end of addition for FREESURFER
+
+install(TARGETS ${PROGRAMS} DESTINATION bin)
+### additions for FREESURFER
+install(TARGETS ${LIBRARY} DESTINATION bin)
+install(TARGETS ${DCM2NIIXFSEXE} DESTINATION bin)

packages/dcm2niix/Info.plist

@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>CFBundleExecutable</key>
+	<string>dcm2niix</string>
+	<key>CFBundleIdentifier</key>
+	<string>com.mricro.dcm2niix</string>
+	<key>CFBundleInfoDictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleName</key>
+	<string>dcm2niix</string>
+	<key>CFBundleShortVersionString</key>
+	<string>1.0</string>
+	<key>CFBundleVersion</key>
+	<string>1</string>
+	<key>CFBundleSupportedPlatforms</key>
+	<array>
+		<string>MacOSX</string>
+	</array>
+	<key>CFBundlePackageType</key>
+	<string>APPL</string>
+</dict>
+</plist>

packages/dcm2niix/charls/License.txt

@@ -0,0 +1,29 @@
+https://github.com/team-charls/charls
+
+Copyright (c) 2007-2010, Jan de Vaan
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of my employer, nor the names of its contributors may be
+  used to endorse or promote products derived from this software without
+  specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.