### Install Local Build of @niivue/dcm2niix

Source: https://github.com/rordenlab/dcm2niix/blob/master/js/README.md

Install a local build of the library by first navigating to the js directory, building the library, packing it, and then installing the generated .tgz file.

```bash
# from dcm2niix root directory
cd js
npm run build
npm pack # will create a .tgz file in the root directory

npm install /path/to/niivue-dcm2niix.tgz
```

--------------------------------

### Install Dependencies Manually

Source: https://github.com/rordenlab/dcm2niix/blob/master/js/README.md

Install project dependencies by navigating to the js directory and running npm install.

```bash
# from dcm2niix root directory
cd js
npm install
```

--------------------------------

### Install @niivue/dcm2niix via npm

Source: https://github.com/rordenlab/dcm2niix/blob/master/js/README.md

Install the library directly from npm using this command.

```bash
npm install @niivue/dcm2niix
```

--------------------------------

### Install Executables and Libraries

Source: https://github.com/rordenlab/dcm2niix/blob/master/console/CMakeLists.txt

Installs the built executables and libraries to their designated directories based on CMake's installation variables.

```cmake
install(TARGETS ${PROGRAMS} DESTINATION ${CMAKE_INSTALL_BINDIR})

if(BUILD_DCM2NIIXFSLIB)
    install(TARGETS ${DCM2NIIXFSLIB} DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
```

--------------------------------

### Install Man Pages

Source: https://github.com/rordenlab/dcm2niix/blob/master/docs/CMakeLists.txt

Installs the generated man pages to the system's man directory.

```cmake
install(DIRECTORY "${SPHINX_OUTPUT_DIR}/"
        DESTINATION "share/man/man1")
```

--------------------------------

### Install dcm2niix with Pip

Source: https://github.com/rordenlab/dcm2niix/blob/master/README.md

Install dcm2niix on Linux, macOS, or Windows using pip.

```bash
python -m pip install dcm2niix
```

--------------------------------

### Compile dcm2niix with CMake

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Utilize cmake for complex builds. This example includes options for ZLIB, CharLS, and OpenJPEG support. Remove '--branch development' to use the stable release.

```bash
git clone --branch development git@github.com:rordenlab/dcm2niix.git
cd dcm2niix
mkdir build && cd build
cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..
make
```

--------------------------------

### Install dcm2niix on Debian Linux

Source: https://github.com/rordenlab/dcm2niix/blob/master/README.md

Install dcm2niix on Debian-based Linux distributions using apt-get.

```bash
sudo apt-get install dcm2niix
```

--------------------------------

### Install dcm2niix with Homebrew (macOS)

Source: https://github.com/rordenlab/dcm2niix/blob/master/README.md

Install dcm2niix on macOS using the Homebrew package manager.

```bash
brew install dcm2niix
```

--------------------------------

### Advanced dcm2niix Command with Options

Source: https://github.com/rordenlab/dcm2niix/blob/master/README.md

An example of invoking dcm2niix with additional options for compression, custom filename formatting, and output directory specification.

```bash
dcm2niix -z y -f %p_%t_%s -o /path/output /path/to/dicom/folder
```

--------------------------------

### Get Help for extract_units.py

Source: https://github.com/rordenlab/dcm2niix/blob/master/BIDS/README.md

Run this command to display the help message for the extract_units.py script, detailing its usage and options.

```bash
extract_units.py -h
```

--------------------------------

### Build Library Manually

Source: https://github.com/rordenlab/dcm2niix/blob/master/js/README.md

Build the JavaScript library after installing dependencies manually. This command is run from the js directory.

```bash
# from dcm2niix root directory
cd js
npm run build
```

--------------------------------

### Install dcm2niix with MacPorts (macOS)

Source: https://github.com/rordenlab/dcm2niix/blob/master/README.md

Install dcm2niix on macOS using the MacPorts package manager.

```bash
sudo port install dcm2niix
```

--------------------------------

### dcm2niibatch Configuration File Example

Source: https://github.com/rordenlab/dcm2niix/blob/master/docs/source/dcm2niibatch.md

This YAML configuration file defines options and lists directories for batch conversion of DICOM files to NIfTI format using dcm2niibatch. Specify input directories, output directories, and desired output filenames.

```yaml
Options:
  isGz:             false
  isFlipY:          false
  isVerbose:        false
  isCreateBIDS:     false
  isOnlySingleFile: false
Files:
    - 
      in_dir:           /path/to/first/folder
      out_dir:          /path/to/output/folder
      filename:         dcemri
    - 
      in_dir:           /path/to/second/folder
      out_dir:          /path/to/output/folder
      filename:         fa3
```

--------------------------------

### Example dcm2niix BIDS Conversion with Hazardous Naming

Source: https://github.com/rordenlab/dcm2niix/blob/master/BidsGuess/README.md

Use the hazardous file naming argument (-f $h) with dcm2niix to create a minimal BIDS structure for validation. This example demonstrates creating a BIDS structure and then validating it using the bids-validator.

```bash
cd ~
mkdir bids
git clone git@github.com:neurolabusc/dcm_qa_pdt2.git
dcm2niix -f %h -w 1 -i y -o ~/bids ~/dcm_qa_pdt2
bids-validator ~/bids
```

--------------------------------

### Build dcm2niix with CMake

Source: https://github.com/rordenlab/dcm2niix/blob/master/README.md

Use this command to build the full-featured dcm2niix version with cmake. Ensure cmake and pkg-config are installed. This method supports JPEG2000 and JPEG-LS formats.

```bash
git clone https://github.com/rordenlab/dcm2niix.git
cd dcm2niix
mkdir build && cd build
cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..
make
```

--------------------------------

### Successful dcm2niix Conversion and Exit Status Check

Source: https://github.com/rordenlab/dcm2niix/blob/master/ERRORS.md

This example demonstrates a successful dcm2niix conversion and how to check its exit status in a shell script. A return value of 0 indicates success.

```bash
>dcm2niix ~/dcm
Chris Rorden's dcm2niiX version v1.0.20200331 Clang11.0.0 (64-bit MacOS)
Found 2 DICOM file(s)
Convert 2 DICOM as ~/dcm/dcm_ax_asc_6 (64x64x35x2)
Conversion required 0.015866 seconds (0.012676 for core code).
>echo $?
0
```

--------------------------------

### Build OpenJPEG 2.1.0 Static Libraries

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Build static libraries for OpenJPEG 2.1.0 with the necessary flag for dcm2niix compatibility. Ensure OpenJPEG is installed via your system's package manager or built from source.

```bash
cmake -DBUILD_SHARED_LIBS:bool=off -DOPJ_DISABLE_TPSOT_FIX:bool=on .
 make
 sudo make install
```

--------------------------------

### MINGW Build with Static Libgcc and ZLib Disabled

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Compile dcm2niix for MinGW on Windows, disabling ZLIB support and including static libgcc libraries. This ensures the executable can run on systems without MinGW installed.

```bash
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 nii_foreign.cpp -o dcm2niix -static-libgcc
```

--------------------------------

### Run Demo

Source: https://github.com/rordenlab/dcm2niix/blob/master/js/README.md

Execute a simple demo to test the functionality of the @niivue/dcm2niix library.

```bash
npm run demo
```

--------------------------------

### Simple Build with Make

Source: https://github.com/rordenlab/dcm2niix/blob/master/CLAUDE.md

This command performs a simple build of dcm2niix using Make, without optional decoders. Navigate to the 'console' directory first.

```bash
cd console && make
```

--------------------------------

### Quick Build with CMake

Source: https://github.com/rordenlab/dcm2niix/blob/master/CLAUDE.md

Use this command to perform a quick build of dcm2niix with full features enabled via CMake. Ensure you are in the project's root directory.

```bash
mkdir build && cd build
cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..
make
```

--------------------------------

### Install dcm2niix with Conda

Source: https://github.com/rordenlab/dcm2niix/blob/master/README.md

Install dcm2niix on Linux, macOS, or Windows using Conda from the conda-forge channel.

```bash
conda install -c conda-forge dcm2niix
```

--------------------------------

### dcm2niix Help Command

Source: https://github.com/rordenlab/dcm2niix/blob/master/README.md

Use this command to display all available options and help information for dcm2niix.

```bash
dcm2niix -h
```

--------------------------------

### Example DICOM Tags and Calculations for GE EPI Data

Source: https://github.com/rordenlab/dcm2niix/blob/master/GE/README.md

An example demonstrating the extraction of relevant DICOM tags and the step-by-step calculation of TotalReadoutTime for a specific GE EPI scan.

```plaintext
(0018,1310) US 128\0\0\128                                 #   8, 4 AcquisitionMatrix
(0018,0022) CS [SAT_GEMS\MP_GEMS\EPI_GEMS\ACC_GEMS\PFF\FS] #  42, 6 ScanOptions
(0043,102c) SS 636                                         #   2, 1 EchoSpacing
(0043,1083) DS [0.666667\1]                                #  10, 2 Acceleration
```

```plaintext
ASSET_R_factor = 1.5 (reciprocal of 1st value in "0043,1083")
AcquisitionMatrixPE = 128 (3rd or 4th value in "0018,1310" (whichever is non-zero))
EchoSpacingMicroSecondsGE = 636 (us)
Round_factor = 4 (because "0018,0022" contains "PFF"; otherwise = 2)
NotPhysicalNumberOfAcquiredPELinesGE = (ceil((1/4) * 128 / 1.5) * 4) = 88
NotPhysicalTotalReadOutTimeGE = (88 - 1) * 636 * 1e-6 = 0.055332 (sec)
EffectiveEchoSpacing = 0.055332 / (128 - 1) = 0.435685e-3 (sec) 
TotalReadoutTime = 0.435685e-3 * (128 - 1) = 0.055332 (sec)
```

--------------------------------

### Compile dcm2niix with Make

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Use these commands to download and compile dcm2niix using the make build system. Remove '--branch development' to use the stable release.

```bash
git clone --branch development git@github.com:rordenlab/dcm2niix.git
cd dcm2niix/console
make
```

--------------------------------

### Configure Sphinx Directories

Source: https://github.com/rordenlab/dcm2niix/blob/master/docs/CMakeLists.txt

Sets up the necessary directories for Sphinx, including source, build, cache, and output directories.

```cmake
set(SPHINX_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/source")
set(SPHINX_BUILD_DIR "${CMAKE_CURRENT_BINARY_DIR}/build")
set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/doctrees")
set(SPHINX_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/man")
```

--------------------------------

### Compile with Debugging Symbols using CMake

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Use this command to compile dcm2niix with debugging symbols enabled. Ensure CMake is installed and configured.

```bash
cmake -DUSE_OPENJPEG=ON -DCMAKE_CXX_FLAGS=-g .. && make
```

--------------------------------

### Configure Zlib Implementation

Source: https://github.com/rordenlab/dcm2niix/blob/master/console/CMakeLists.txt

Allows selection of zlib implementation (Miniz, System, Custom) and configures build settings accordingly. If a custom zlib is chosen, ZLIB_ROOT must be specified.

```cmake
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()
```

--------------------------------

### Initialize and Convert DICOM Files in Browser

Source: https://github.com/rordenlab/dcm2niix/blob/master/js/README.md

Instantiate the Dcm2niix class, initialize the WASM module, and then process a list of files from an HTML input element. Ensure the input element has 'webkitdirectory' and 'multiple' attributes. The result is a list of browser File Objects.

```javascript
// assuming you have an html input element to get directories.
// <input type="file" id="fileInput" webkitdirectory multiple>
import { Dcm2niix } from '@niivue/dcm2niix';

// use the jpeg import to load jpegls and j2k build of dcm2niix
// import { Dcm2niix } from '@niivue/dcm2niix/jpeg';

const dcm2niix = new Dcm2niix();
// call the init() method to load the wasm before processing any data
await dcm2niix.init();
// fileInput is the id of the input element with options: webkitdirectory and multiple
fileInput.addEventListener('change', async (event) => {
    inputFileList = event.target.files;
});
// inputFileList is the value from the input element with options: webkitdirectory and multiple
const resultFileList = await dcm2niix.input(inputFileList).run()  
console.log(resultFileList);
// Do something with the resultFileList (normal browser File Objects)
// perhaps view them with @niivue/niivue :)
```

--------------------------------

### Custom Diffusion Directions File Format

Source: https://github.com/rordenlab/dcm2niix/blob/master/Philips/README.md

This is an example of a custom text file format for specifying diffusion directions and b-values, compatible with Philips FiberTrak.

```text
MyCustomDirections
0.000	0.000	1.000	0
0.049	-0.919	-0.391	1000
0.726	0.301	-0.618	1000
-0.683	0.255	-0.684	1000
0.845	-0.502	-0.186	1000
-0.73	-0.619	-0.288	1000
-0.051	0.039	0.998	1000
-0.018	0.871	-0.491	1000
-0.444	0.494	0.747	1000
-0.989	-0.086	-0.116	1000
1.000	0.000	0.000	0

```

--------------------------------

### Process Selected Files with dcm2niix

Source: https://github.com/rordenlab/dcm2niix/blob/master/js/index.html

Handles file selection via an input element and processes the selected files using dcm2niix WASM upon a button click. It initializes the WASM module, applies a compression option ('z' for gzip), runs the conversion, and creates download links for the output files. Includes basic error handling and performance timing.

```javascript
let selectedFiles = null;

fileInput.addEventListener('change', async (event) => {
  selectedFiles = event.target.files;
  console.log(selectedFiles);
});

processButton.addEventListener('click', async () => {
  status.textContent = 'Processing...';
  try {
    console.log('Initializing dcm2niix wasm...');
    const dcm2niix = new Dcm2niix();
    await dcm2niix.init();
    console.log('dcm2niix wasm initialized.');
    const t0 = performance.now();
    const inputFileList = selectedFiles
    const resultFileList = await dcm2niix.input(inputFileList).z('y').run()
    console.log(resultFileList);
    const t1 = performance.now();
    console.log("dcm2niix wasm took " + (t1 - t0) + " milliseconds.")
    resultFileList.forEach((resultFile, index) => {
      let url = URL.createObjectURL(resultFile);
      const downloadLink = document.createElement('a');
      downloadLink.href = url;
      downloadLink.download = resultFile.name;
      downloadLink.textContent = `Download ${resultFile.name}`;
      downloadLink.style.display = 'block';
      document.body.appendChild(downloadLink);
    });
    status.textContent = 'Processing complete!';
  } catch (error) {
    console.error('Processing failed:', error);
    status.textContent = 'Processing failed. Please check the console for details.';
  } finally {
    processButton.disabled = false;
  }
});
```

--------------------------------

### Compile dcm2niix with Jasper and libjpeg

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Compile dcm2niix with JPEG2000 decompression support using the Jasper library and libjpeg. This command assumes Jasper and libjpeg are installed.

```bash
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 nii_foreign.cpp -s -o dcm2niix -ljasper -ljpeg
```

--------------------------------

### Compile dcm2niix with OpenJPEG (Default)

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Compile dcm2niix with JPEG2000 decompression support using the OpenJPEG library. This command assumes OpenJPEG is installed and discoverable by the compiler.

```bash
g++ -O3 -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -o dcm2niix -lopenjp2
```

--------------------------------

### Run Batch Conversion with dcm2niibatch

Source: https://github.com/rordenlab/dcm2niix/blob/master/BATCH.md

Execute the batch conversion process by providing the path to your YAML configuration file. Ensure the configuration file specifies all necessary options and file paths for the conversion.

```bash
dcm2niibatch batch_config.yml
```

--------------------------------

### Validate Universal Binary Architecture on macOS

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Use the 'file' command to verify that the compiled dcm2niix executable supports the intended architectures.

```bash
file ./dcm2niix
```

--------------------------------

### Philips DICOM Tag Examples

Source: https://github.com/rordenlab/dcm2niix/blob/master/Philips/README.md

Sample DICOM tags from a Philips enhanced image illustrating the detection of DIRECTIONAL, ISOTROPIC, and NONE image types using Diffusion Directionality and Dimension Index Values.

```dicom
(0018,9075) CS [DIRECTIONAL]
(0018,9089) FD 1\0\0
(0018,9087) FD 1000
(0020,9157) UL 1\1\2\32
```

```dicom
(0018,9075) CS [ISOTROPIC]
(0018,9087) FD 1000
(0020,9157) UL 1\2\1\33
```

```dicom
(0018,9075) CS [NONE]
(0018,9087) FD 0
(0020,9157) UL 1\1\2\33
```

--------------------------------

### Enable Jasper Support

Source: https://github.com/rordenlab/dcm2niix/blob/master/console/CMakeLists.txt

Finds and links against the Jasper library if USE_JASPER is enabled.

```cmake
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()
```

--------------------------------

### Canon V6.1 DICOM DWI Example (Classic/Enhanced)

Source: https://github.com/rordenlab/dcm2niix/blob/master/Canon/README.md

Shows the diffusion properties reported in Canon DICOM images from software version 6.1, where both DiffusionBValue and DiffusionGradientOrientation are in public tags for both classic and enhanced DICOMs.

```text
(0018,9087) FD 1500                                     #   8, 1 DiffusionBValue
(0018,9089) FD 0.29387456178665161\-0.95365142822265625\-0.064700603485107422 #  24, 3 DiffusionGradientOrientation
```

--------------------------------

### BidsGuess JSON Output Example

Source: https://github.com/rordenlab/dcm2niix/blob/master/BidsGuess/README.md

Inspect the JSON sidecar files generated by dcm2niix to see the 'BidsGuess' field, which suggests likely BIDS data types and entities. This output is for understanding the feature's suggestions.

```json
	"BidsGuess": ["anat","_acq-tse2_run-3_PDw"],
	"BidsGuess": ["anat","_acq-tse2_run-3_T2w"]
```

--------------------------------

### Create Universal Binaries for macOS

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Compile dcm2niix for different architectures on macOS and combine them into a universal binary using lipo. This allows the executable to run on PowerPC, Intel, and Apple Silicon (M1) CPUs.

```bash
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 nii_foreign.cpp -arch i386 -o dcm2niix32 g++ -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableOpenJPEG -Wl,-stack_size -Wl,3f00000
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 nii_foreign.cpp -o dcm2niix64 g++ -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableOpenJPEG -Wl,-stack_size -Wl,3f00000
lipo -create dcm2niix32 dcm2niix64 -o dcm2niix
```

--------------------------------

### ZLIB Build with MiniZ Disabled

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Compile dcm2niix using g++ with ZLIB support and MiniZ disabled. This command links against the ZLIB library and specifies include paths.

```bash
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 nii_foreign.cpp -o dcm2niix -lz -DmyDisableMiniZ
```

--------------------------------

### Canon Classic DICOM DWI Example (V6.0)

Source: https://github.com/rordenlab/dcm2niix/blob/master/Canon/README.md

Illustrates the diffusion properties reported in Canon classic DICOM images from software version 6.0, where DiffusionBValue is in a public tag and gradient orientation is in the Image Comments tag.

```text
(0018,9087) FD 1500                                     #   8, 1 DiffusionBValue
(0020,4000) LT [b=1500(0.445,0.000,0.895)]              #  26, 1 ImageComments
```

--------------------------------

### Enable JNIfTI Support

Source: https://github.com/rordenlab/dcm2niix/blob/master/console/CMakeLists.txt

Adds definitions and source files for JNIfTI support if the USE_JNIFTI option is enabled.

```cmake
option(USE_JNIFTI "Build with JNIfTI support" ON)
if(USE_JNIFTI)
    add_definitions(-DmyEnableJNIFTI)
    set(DCM2NIIX_SRCS ${DCM2NIIX_SRCS} cJSON.cpp base64.cpp)
endif()
```

--------------------------------

### Customizing dcm2niix Output File Names

Source: https://github.com/rordenlab/dcm2niix/blob/master/PARREC/README.md

Use the -f argument with dcm2niix to specify a custom output file name format. The example shows how to use '%p' (protocol name) and '%s' (series number) for Philips PAR/REC files. Refer to the documentation for a full list of available format specifiers.

```bash
dcm2niix -f %p_%s ~/myParDir
```

--------------------------------

### ZLIB Build with OpenJPEG Disabled

Source: https://github.com/rordenlab/dcm2niix/blob/master/COMPILE.md

Compile dcm2niix using g++ with ZLIB support and OpenJPEG disabled. This command also sets a larger stack size.

```bash
g++ -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableOpenJPEG -Wl,-stack_size -Wl,3f00000
```

--------------------------------

### Compile dcm2niix with CharLS v1 (C++03)

Source: https://github.com/rordenlab/dcm2niix/blob/master/console/charls/README.md

Compile dcm2niix with CharLS version 1 support. Requires C++03 and the `myEnableJPEGLS1` flag. This version is not included with dcm2niix and must be downloaded separately. OpenJPEG support is disabled.

```bash
g++ -I. -std=c++03 -DmyEnableJPEGLS1  charls1/header.cpp charls1/jpegls.cpp charls1/jpegmarkersegment.cpp charls1/interface.cpp  charls1/jpegstreamwriter.cpp main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp  -o dcm2niix -DmyDisableOpenJPEG
```