### Install Lazarus and Dependencies in Docker

Source: https://github.com/rordenlab/mricrogl/blob/master/DOCKER.md

Installs Lazarus IDE, Free Pascal compiler, Git, and necessary libraries within a Docker container. This prepares the environment for compiling MRIcroGL.

```bash
cd ~
wget --no-check-certificate https://sourceforge.net/projects/lazarus/files/Lazarus%20Linux%20amd64%20DEB/Lazarus%202.0.4/lazarus-project_2.0.4-0_amd64.deb
wget --no-check-certificate https://sourceforge.net/projects/lazarus/files/Lazarus%20Linux%20amd64%20DEB/Lazarus%202.0.4/fpc-src_3.0.4-2_amd64.deb
wget --no-check-certificate https://sourceforge.net/projects/lazarus/files/Lazarus%20Linux%20amd64%20DEB/Lazarus%202.0.4/fpc-laz_3.0.4-1_amd64.deb
apt-get update
apt -yq install ./fpc-src_3.0.4-2_amd64.deb
apt -yq install ./fpc-laz_3.0.4-1_amd64.deb 
apt -yq install ./lazarus-project_2.0.4-0_amd64.deb 
apt-get -yq install git
apt-get -yq install libgl1-mesa-dev
apt-get install build-essential 
```

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

### Launch MRIcroGL with a Python script from Python

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

This example demonstrates launching MRIcroGL and executing a Python script using the subprocess module in Python. Adjust the path to the MRIcroGL executable as necessary.

```python
import subprocess
subprocess.call(['/Users/rorden/tst/MRIcroGL12/MRIcroGL.app/Contents/MacOS/MRIcroGL','myscript.py'])
```

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

### Launch MRIcroGL with a Python script from Matlab

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

This example shows how to execute a Python script using MRIcroGL from a Matlab environment. Ensure the MRIcroGL executable is in your system's PATH or provide the full path.

```matlab
script = 'myscript.py';
exe = 'mricrogl';
if ~exist(exe,'file'), error('Unable to find application "%s"', exe); end
cmd = sprintf('%s "%s"', exe, script);
system(cmd);
```

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

### Choose Rendering Shader

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Selects the shading algorithm for rendering. For example, 'mip' renders a maximum intensity projection.

```python
shadername(name)
```

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

### Compile MRIcroGL with Command Line (Linux/Windows)

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

Commands to clone the MRIcroGL repository and compile it using lazbuild for Linux (QT5) or Windows. Ensure Lazarus 2.0.6 or later is installed and lazbuild is available.

```bash
git clone https://github.com/rordenlab/MRIcroGL.git
lazbuild --build-ide= --add-package lazopenglcontext ./Python27-for-Lazarus/python4lazarus/python4lazarus_package.lpk
cd MRIcroGL
lazbuild  -B MRIcroGL.lpr
```

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

### Run Interactive MRIcroGL Docker Container

Source: https://github.com/rordenlab/mricrogl/blob/master/DOCKER.md

Starts an interactive Docker container, allowing direct access to a bash shell within the jgoerzen/debian-base-standard environment. Use this to perform compilation steps.

```bash
docker run -it jgoerzen/debian-base-standard /bin/bash
```

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

### Get MRIcroGL Version

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Returns a string representing the current version of the MRIcroGL application.

```python
version()
```

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

### Compile MRIcroGL with Command Line (macOS)

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

Commands to clone the MRIcroGL repository and compile it using lazbuild for macOS, specifying the modern Cocoa widgetset. Ensure Lazarus 2.0.6 or later is installed and lazbuild is available.

```bash
git clone https://github.com/rordenlab/MRIcroGL.git
cd MRIcroGL
lazbuild  -B --ws=cocoa MRIcroGL.lpi
```

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

### Set Shader Light Azimuth and Elevation

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Positions the light source used for rendering. For example, `shaderlightazimuthelevation(0,45)` places light 45 degrees above.

```python
shaderlightazimuthelevation(a,e)
```

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

### Mosaic View - Single Rendering

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Displays multiple slices of the brain simultaneously using the mosaic view. This example loads a background image and overlays, then configures the mosaic layout.

```python
import gl
gl.resetdefaults()
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1,50)
#open overlay: show negative regions
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname (2,"3blue")
gl.mosaic("A L+ H -0.1 -24 -16 16 40; 48 56 S X R 0")
```

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

### Convert Colormap to .clut Format

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

Use this command to convert a specific colormap (e.g., 'davos') from the 'cmap' library into an MRIcroGL-compatible .clut file. Ensure 'cmap' is installed.

```bash
pip install cmap
python color2clut.py davos
```

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

### Run Detached MRIcroGL Docker Container

Source: https://github.com/rordenlab/mricrogl/blob/master/DOCKER.md

Starts a Docker container in detached mode, named 'name', and configures it to stop with SIGPWR. This container is based on the jgoerzen/debian-base-standard image.

```bash
docker run -td --stop-signal=SIGPWR --name=name jgoerzen/debian-base-standard
```

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

### Configure zlib for macOS

Source: https://github.com/rordenlab/mricrogl/blob/master/x86_64-darwin/README.txt

Run the configure script to prepare the build environment. Edit the Makefile to specify the minimum macOS version.

```bash
./configure
```

```bash
edit makefile for "-mmacosx-version-min=10.8"
```

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

### Load Images with Command Line Options

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

Specify images, colormaps, and display ranges directly from the command line when launching MRIcroGL. Options are similar to fsleyes.

```bash
MRIcroGL -std -dr 2000 6000   motor -cm actc -dr 2 4
```

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

### Load Background and Overlays

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Loads a background image and two overlays, one for positive and one for negative regions. Adjusts min/max values, opacity, and color for each overlay. Uncomment the last line to view 2D slices.

```python
import gl
gl.resetdefaults()
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1,50)
#open overlay: show negative regions
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname (2,"3blue")
#gl.orthoviewmm(37,-14,47)
```

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

### Adjust Shader Property

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Sets the level of a specific shader property. For example, 'gl.shaderadjust('edgethresh', 0.6)' adjusts the edge threshold.

```python
shaderadjust(sliderName, sliderValue)
```

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

### Set Color Scheme Range from Zero

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Determines if the color scheme for a layer starts from zero (1) or a threshold value (0).

```python
colorfromzero(layer, isFromZero)
```

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

### Compile zlib

Source: https://github.com/rordenlab/mricrogl/blob/master/x86_64-darwin/README.txt

Execute the make command to compile the zlib library with the specified CFLAGS.

```bash
make
```

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

### Window Positioning and Sizing

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Set the position and dimensions of the application window.

```APIDOC
## windowposition

### Description
Set the left, top, width, and height for the application window.

### Method
windowposition(l,t,w,h)

### Parameters
- **l** (integer) - The left position of the window.
- **t** (integer) - The top position of the window.
- **w** (integer) - The width of the window.
- **h** (integer) - The height of the window.
```

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

### Load Overlay Image

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Loads an image as an overlay on top of the existing background or other overlays. Specify the filename.

```python
overlayload(filename)
```

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

### Create MRIcroGL Distribution

Source: https://github.com/rordenlab/mricrogl/blob/master/DOCKER.md

Creates a distribution directory and copies the compiled MRIcroGL executable and its resources into it. This prepares MRIcroGL for deployment.

```bash
mkdir ~/distro  
mkdir ~/distro/MRIcroGL
cp ./MRIcroGL ~/distro/MRIcroGL/MRIcroGL
cp -a ./Resources/ ~/distro/MRIcroGL
```

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

### Compile zlib object files (Basic)

Source: https://github.com/rordenlab/mricrogl/blob/master/x86_64-win64/README.txt

Compiles individual C source files for zlib into object files using GCC with -O3 optimization. This is a standard compilation process for creating object files.

```bash
gcc -O3  -c -o adler32.o adler32.c
```

```bash
gcc -O3  -c -o crc32.o crc32.c
```

```bash
gcc -O3  -c -o deflate.o deflate.c  -msse4
```

```bash
gcc -O3  -c -o inffast.o inffast.c
```

```bash
gcc -O3  -c -o inflate.o inflate.c
```

```bash
gcc -O3  -c -o inftrees.o inftrees.c
```

```bash
gcc -O3  -c -o trees.o trees.c
```

```bash
gcc -O3  -c -o zutil.o zutil.c
```

```bash
gcc -O3  -c -o adler32_simd.o adler32_simd.c
```

```bash
gcc -O3  -c -o crc32_simd.o crc32_simd.c
```

```bash
gcc -O3  -c -o inffast_chunk.o inffast_chunk.c
```

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

### Specify LLVMgold.so Plugin with FPC Options

Source: https://github.com/rordenlab/mricrogl/blob/master/MRIcroGL_llvm_linux.txt

Pass linker options to the Free Pascal Compiler (FPC) to specify the LLVMgold.so plugin. This ensures the correct LLVM version is used for LTO processing.

```bash
-k-plugin -k/usr/lib/llvm-10/lib/LLVMgold.so
```

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

### Reset Settings to Defaults

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Reverts all application settings to their default values. Useful for troubleshooting.

```python
resetdefaults()
```

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

### Download MRIcroGL Latest Version (Windows)

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

Use this command to download the latest version of MRIcroGL for Windows.

```bash
curl -fLO https://github.com/rordenlab/MRIcroGL/releases/latest/download/MRIcroGL_windows.zip
```

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

### Compile zlib object files (with SIMD and specific flags)

Source: https://github.com/rordenlab/mricrogl/blob/master/x86_64-win64/README.txt

Compiles individual C source files for zlib into object files using GCC with -O3 optimization and various SIMD (SSE4, SSSE3, SSE2) and other specific flags. These flags enable advanced instruction sets for performance.

```bash
gcc -O3  -c -o adler32.o adler32.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o crc32.o crc32.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o deflate.o deflate.c  -msse4  -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o inffast.o inffast.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o inflate.o inflate.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o inftrees.o inftrees.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o trees.o trees.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o zutil.o zutil.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o adler32_simd.o adler32_simd.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o crc32_simd.o crc32_simd.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

```bash
gcc -O3  -c -o inffast_chunk.o inffast_chunk.c -DHAS_PCLMUL -mpclmul -DHAS_SSE42 -msse4.2 -DADLER32_SIMD_SSSE3 -mssse3 -DINFLATE_CHUNK_SIMD_SSE2 -msse2 -DINFLATE_CHUNK_READ_64LE -O3  -DHAVE_HIDDEN
```

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

### Save Screen Display as Bitmap

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Saves the current view as a bitmap image file. Specify the desired filename (e.g., 'test.png').

```python
savebmp(pngName)
```

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

### Download MRIcroGL Latest Version (Linux)

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

Use this command to download the latest version of MRIcroGL for Linux.

```bash
curl -fLO https://github.com/rordenlab/MRIcroGL/releases/latest/download/MRIcroGL_linux.zip
```

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

### Build Lazarus Packages

Source: https://github.com/rordenlab/mricrogl/blob/master/DOCKER.md

Builds the Python-for-Lazarus package and the lazopenglcontext package using lazbuild. These are required for MRIcroGL functionality.

```bash
lazbuild --add-package ~/Python-for-Lazarus/python4lazarus/python4lazarus_package.lpk  --build-ide=
lazbuild --add-package lazopenglcontext --build-ide=
```

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

### Load Background Image

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Closes any currently open images and loads a new image as the background layer. Specify the image file name.

```python
loadimage(imageName)
```

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

### Jagged vs. Blurry Interpolation

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Demonstrates the difference between nearest-neighbor (jagged) and trilinear (blurry) interpolation when re-slicing overlays to match background resolution. Prints a note indicating which surface is jagged.

```python
import gl
gl.resetdefaults()
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayloadsmooth(1);
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1,50)
#open overlay: show negative regions
gl.overlayloadsmooth(0);
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname (2,"3blue")
gl.overlayloadsmooth(1);
print("n.b. Blue surface is jagged (smoothing off)")
```

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

### Run Python Script with MRIcroGL

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

Execute a Python script to control MRIcroGL. This allows for automation and precise results.

```bash
mricrogl myscript.py
```

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

### List mricrogl Python Functions

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Prints all built-in Python functions available in the gl module, along with their docstrings. This is useful for discovering available commands and their usage.

```python
import gl
print(gl.__doc__)
for key in dir( gl ):
  if not key.startswith('_'):
    x = getattr( gl, key ).__doc__
    print(key+' (built-in function): ')
    print(x)
```

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

### Image and Overlay Management

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Functions for loading, saving, and managing images and overlays.

```APIDOC
## loadimage

### Description
Closes all open images and loads a new background image.

### Method
`loadimage(imageName)`

### Parameters
- **imageName** (string) - The path to the image file.

## overlaycloseall

### Description
Closes all currently open overlays.

### Method
`overlaycloseall()`

## overlayload

### Description
Loads an image as an overlay on top of existing images.

### Method
`overlayload(filename)`

### Parameters
- **filename** (string) - The path to the overlay image file.

## overlayloadsmooth

### Description
Determines whether future `overlayload()` calls use smooth or jagged interpolation.

### Method
`overlayloadsmooth(v)`

### Parameters
- **v** (int) - 1 to use smooth interpolation, 0 for jagged interpolation.

## overlaymaskwithbackground

### Description
Controls whether overlay voxels that are transparent in the background image are hidden.

### Method
`overlaymaskwithbackground(v)`

### Parameters
- **v** (int) - 1 to hide transparent voxels, 0 to show them.

## savebmp

### Description
Saves the current screen display as a bitmap image.

### Method
`savebmp(pngName)`

### Parameters
- **pngName** (string) - The desired filename for the bitmap image (e.g., 'test.png').
```

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

### Overlay Management

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Functions to manage open overlays, including closing all, counting them, and loading new ones.

```APIDOC
## overlaycloseall

### Description
Close all open overlays.

### Method
overlaycloseall()
```

```APIDOC
## overlaycount

### Description
Return the number of overlays currently open.

### Method
overlaycount() -> integer
```

```APIDOC
## overlayload

### Description
Load an image as an overlay on top of prior images.

### Method
overlayload(filename)

### Parameters
- **filename** (string) - The path to the image file to load.
```

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

### View Modes

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Set the display mode for the rendered volume.

```APIDOC
## view

### Description
Set the display mode for the volume. Can display Axial (1), Coronal (2), Sagittal (4), Flipped Sagittal (8), MPR (16), Mosaic (32), or Rendering (64). Multiple modes can be combined using bitwise OR.

### Method
view(v)

### Parameters
- **v** (integer) - A bitmask representing the desired view mode(s).
```

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

### Utility and Application Functions

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Miscellaneous functions for user interaction, application control, and information retrieval.

```APIDOC
## colorbarposition

### Description
Sets the position of the color bar.

### Method
`colorbarposition(p)`

### Parameters
- **p** (int) - Position code: 0=off, 1=top, 2=right.

## colorbarsize

### Description
Changes the width of the color bar.

### Method
`colorbarsize(p)`

### Parameters
- **p** (float) - Fraction of screen width used by the color bar (0.01 to 0.5).

## cutout

### Description
Removes a sector from the volume.

### Method
`cutout(L, A, S, R, P, I)`

### Parameters
- **L** (float) - Parameter L.
- **A** (float) - Parameter A.
- **S** (float) - Parameter S.
- **R** (float) - Parameter R.
- **P** (float) - Parameter P.
- **I** (float) - Parameter I.

## extract

### Description
Removes haze from the volume.

### Method
`extract(Otsu, Dil, One)`

### Parameters
- **Otsu** (float) - Otsu threshold value.
- **Dil** (int) - Dilation value.
- **One** (int) - Parameter One.

## hiddenbycutout

### Description
Determines if the cutout operation hides or shows a layer.

### Method
`hiddenbycutout(layer, isHidden)`

### Parameters
- **layer** (int) - The target layer (0 for background).
- **isHidden** (int) - 1 to hide, 0 to show.

## linewidth

### Description
Sets the thickness of crosshairs used on 2D slices.

### Method
`linewidth(wid)`

### Parameters
- **wid** (float) - The desired thickness of the crosshairs.

## modalmessage

### Description
Shows a message in a dialog box and pauses script execution until the user presses 'OK'.

### Method
`modalmessage(msg)`

### Parameters
- **msg** (string) - The message to display.

## mosaic

### Description
Creates a series of 2D slices.

### Method
`mosaic(mosString)`

### Parameters
- **mosString** (string) - String defining the mosaic parameters.

## overlaymaskwithbackground

### Description
Hides (1) or shows (0) overlay voxels that are transparent in the background image.

### Method
`overlaymaskwithbackground(v)`

### Parameters
- **v** (int) - 1 to hide, 0 to show.

## quit

### Description
Terminates the MRIcroGL application.

### Method
`quit()`

## resetdefaults

### Description
Reverts all settings to their default values.

### Method
`resetdefaults()`

## scriptformvisible

### Description
Shows or hides the scripting window.

### Method
`scriptformvisible(visible)`

### Parameters
- **visible** (int) - 1 to show the scripting window, 0 to hide it.

## toolformvisible

### Description
Shows or hides the tool panel.

### Method
`toolformvisible(visible)`

### Parameters
- **visible** (int) - 1 to show the tool panel, 0 to hide it.

## version

### Description
Returns the current version of MRIcroGL.

### Method
`version()`

### Returns
- **string**: The version string of MRIcroGL.
```

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

### Compile MRIcroGL

Source: https://github.com/rordenlab/mricrogl/blob/master/DOCKER.md

Compiles the MRIcroGL application using lazbuild. This command builds the main MRIcroGL project file.

```bash
cd MRIcroGL12
lazbuild -B ./MRIcroGL.lpr
```

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

### Batch Convert Default Colormaps

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

Run the conversion script without arguments to batch-convert a default set of colormaps. The optional '-t' argument can adjust interpolation tolerance for balancing node count and color precision.

```bash
python color2clut.py
```

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

### Clone MRIcroGL and Related Repositories

Source: https://github.com/rordenlab/mricrogl/blob/master/DOCKER.md

Clones the MRIcroGL source code and other necessary repositories (Metal-Demos, Python-for-Lazarus) into the Docker container. This step is crucial for compilation.

```bash
git clone https://github.com/rordenlab/MRIcroGL12.git
git clone https://github.com/neurolabusc/Metal-Demos
git clone https://github.com/Alexey-T/Python-for-Lazarus.git
```

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

### Linux MRIcroGL Deployment Paths

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

Specifies the order of directories MRIcroGL searches for its Resources folder on Linux systems when not found in the same directory as the executable or via the MRICROGL_DIR environment variable.

```bash
 /opt/MRIcroGL/Resources
  /opt/MRIcroGL
  /opt/MRIcroGL/Resources
  /opt/MRIcroGL
  /usr/local/MRIcroGL/Resources
  /usr/local/MRIcroGL
  /usr/local/MRIcroGL/Resources
  /usr/local/MRIcroGL
  /usr/local/share/MRIcroGL/Resources
  /usr/local/share/MRIcroGL
  /usr/local/share/MRIcroGL/Resources
  /usr/local/share/MRIcroGL
 
```

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

### Set Overlay Blending Mode

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Chooses the blending mode for overlaying images. Use additive (1) or multiplicative (0) blending.

```python
overlayadditiveblending(v)
```

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

### Download MRIcroGL Latest Version (macOS)

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

Use this command to download the latest version of MRIcroGL for macOS.

```bash
curl -fLO https://github.com/rordenlab/MRIcroGL/releases/latest/download/MRIcroGL_macOS.dmg
```

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

### Mosaic View - Multiple Renderings

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Configures the mosaic view to show multiple renderings simultaneously, including axial, coronal, and sagittal views with different rendering options. Sets a white background and positions the color bar.

```python
import gl
gl.resetdefaults()
gl.backcolor(255, 255, 255)
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1,50)
#open overlay: show negative regions
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname (2,"3blue")
gl.colorbarposition(0)
#"a"xial, "c"oronal and "s"agittal "r"enderings
gl.mosaic("A R 0 C R 0 S R 0; A R -0 C R -0 S R -0")
```

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

### Image Loading and Display Functions

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Functions for loading and displaying images.

```APIDOC
## loadimage

### Description
Closes all open images and loads a new background image.

### Method
`loadimage(imageName)`

### Parameters
- **imageName** (string) - The path to the image file to load.
```

```APIDOC
## mosaic

### Description
Creates a series of 2D slices arranged in a mosaic.

### Method
`mosaic(mosString)`

### Parameters
- **mosString** (string) - A string defining the mosaic layout.
```

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

### Control Scripting Window Visibility

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Shows (1) or hides (0) the scripting window, allowing more space for the main viewer.

```python
scriptformvisible (visible)
```

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

### Instance Synchronization

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Synchronize the view across multiple instances of MRIcroGL.

```APIDOC
## yoke

### Description
Synchronize (1) or de-synchronize (0) instances so that different instances show the same view.

### Method
yoke(v)

### Parameters
- **v** (integer) - 1 to yoke instances, 0 to de-synchronize.
```

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

### Image Saving

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Save the current display or background image to various file formats.

```APIDOC
## savebmp

### Description
Save the current screen display as a bitmap image.

### Method
savebmp(pngName)

### Parameters
- **pngName** (string) - The filename (e.g., 'test.png') to save the bitmap as.
```

```APIDOC
## saveimg

### Description
Save the background image (layer 0) to disk. The file extension determines the format.

### Method
saveimg(filename)

### Parameters
- **filename** (string) - The desired filename, including the extension (e.g., 'test.nii', 'test.osp', 'test.bvox'). Supported extensions: .nii (NIfTI), .osp (ospray), .bvox (blender).
```

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

### Color and Appearance Functions

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Functions to control background color, color schemes, and overlay blending.

```APIDOC
## backcolor

### Description
Changes the background color.

### Method
`backcolor(r, g, b)`

### Parameters
- **r** (int) - Red component (0-255).
- **g** (int) - Green component (0-255).
- **b** (int) - Blue component (0-255).

## colorfromzero

### Description
Determines if the color scheme display range starts from zero or a threshold value.

### Method
`colorfromzero(layer, isFromZero)`

### Parameters
- **layer** (int) - The target layer (0 for background).
- **isFromZero** (int) - 1 to start from zero, 0 to start from threshold.

## colorname

### Description
Sets the colorscheme for a specified overlay to a named scheme.

### Method
`colorname(layer, colorName)`

### Parameters
- **layer** (int) - The target layer (0 for background layer).
- **colorName** (string) - The name of the colorscheme.

## linecolor

### Description
Sets the color of the crosshairs.

### Method
`linecolor(r, g, b)`

### Parameters
- **r** (int) - Red component (0-255).
- **g** (int) - Green component (0-255).
- **b** (int) - Blue component (0-255).

## minmax

### Description
Sets the color range for an overlay.

### Method
`minmax(layer, min, max)`

### Parameters
- **layer** (int) - The target layer (0 for background).
- **min** (float) - The minimum value for the color range.
- **max** (float) - The maximum value for the color range.

## opacity

### Description
Adjusts the transparency of a layer.

### Method
`opacity(layer, opacityPct)`

### Parameters
- **layer** (int) - The target layer (0 for background, 1 for 1st overlay).
- **opacityPct** (int) - Opacity percentage (0=transparent, 100=opaque).

## overlayadditiveblending

### Description
Merges overlays using additive or multiplicative blending.

### Method
`overlayadditiveblending(v)`

### Parameters
- **v** (int) - 1 for additive blending, 0 for multiplicative blending.
```

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

### Set Overlay Colorscheme by Name

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Applies a named colorscheme to a specified overlay. Layer 0 refers to the background.

```python
colorname(layer, colorName)
```

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

### Set Layer Opacity

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Adjusts the transparency of a layer. 0 is fully transparent, 100 is fully opaque. Layer 0 is the background.

```python
opacity(layer, opacityPct)
```

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

### Graph and Data Loading Functions

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Functions for loading and scaling graph data.

```APIDOC
## graphscaling

### Description
Sets the scaling type for the vertical axis of a graph.

### Method
`graphscaling(type)`

### Parameters
- **type** (number) - Scaling type: 0=raw, 1=demeaned, 2=normalized -1..1, 3=normalized 0..1, 4=percent.
```

```APIDOC
## loadgraph

### Description
Loads a graph from a text file.

### Method
`loadgraph(graphName, add)`

### Parameters
- **graphName** (string) - The name of the graph file (e.g., AFNI .1D, FSL .par, SPM rp_.txt).
- **add** (number, optional) - If 1, the new graph is added to the existing graph; otherwise, it replaces it (default is 0).
```

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

### Cutout with OverlaySurface Shader

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Loads a background image and overlays, then applies a cutout box and the 'OverlaySurface' shader to only display overlays beneath the brain's surface. Sets a white background color.

```python
import gl
gl.resetdefaults()
#open background image
gl.loadimage('spm152')
gl.overlayloadsmooth(1)
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, -2,-5)
gl.colorname(1,'8redyell')
gl.colorfromzero(1,1)
gl.overlayload('spmMotor')
gl.minmax(2, 2,5)
gl.colorname(2,'5winter')
gl.colorfromzero(2,1)
gl.hiddenbycutout(1,1)
gl.cutout(0.5,0.5,0.5,0,1,1)
gl.shadername('OverlaySurface')
gl.backcolor(255,255,255)
```

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

### Scripting Window Visibility

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Control the visibility of the scripting window.

```APIDOC
## scriptformvisible

### Description
Show (1) or hide (0) the scripting window.

### Method
scriptformvisible(visible)

### Parameters
- **visible** (integer) - 1 to show the scripting window, 0 to hide it.
```

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

### Control Tool Panel Visibility

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Shows (1) or hides (0) the tool panel, which contains various editing and manipulation tools.

```python
toolformvisible(visible)
```

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

### Specify LLVMgold.so Plugin for Linker

Source: https://github.com/rordenlab/mricrogl/blob/master/MRIcroGL_llvm_linux.txt

Manually override the LTO plugin location by passing the plugin path to the linker. This is useful when the default symlink points to an incompatible LLVM version.

```bash
-plugin /usr/lib/llvm-10/lib/LLVMgold.so
```

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

### Rendering and Camera Functions

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Functions to control the 3D rendering camera and view.

```APIDOC
## azimuthelevation

### Description
Sets the render camera's azimuthal and elevation angles.

### Method
`azimuthelevation(azi, elev)`

### Parameters
- **azi** (number) - The azimuthal angle.
- **elev** (number) - The elevation angle.
```

```APIDOC
## cameradistance

### Description
Sets the viewing distance from the object.

### Method
`cameradistance(z)`

### Parameters
- **z** (number) - The viewing distance.
```

```APIDOC
## clipazimuthelevation

### Description
Sets a view-point independent clip plane.

### Method
`clipazimuthelevation(depth, azi, elev)`

### Parameters
- **depth** (number) - The depth of the clip plane.
- **azi** (number) - The azimuthal angle for the clip plane.
- **elev** (number) - The elevation angle for the clip plane.
```

```APIDOC
## clipthick

### Description
Sets the thickness of the clip plane slab.

### Method
`clipthick(thick)`

### Parameters
- **thick** (number) - The thickness of the clip plane (0..1).
```

```APIDOC
## orthoviewmm

### Description
Displays three orthogonal slices of the brain at specified millimeter coordinates.

### Method
`orthoviewmm(x, y, z)`

### Parameters
- **x** (number) - The x-coordinate in millimeters.
- **y** (number) - The y-coordinate in millimeters.
- **z** (number) - The z-coordinate in millimeters.
```

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

### Shader Adjustments

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Adjust shader properties and select rendering shaders.

```APIDOC
## shaderadjust

### Description
Set the level of a specific shader property.

### Method
shaderadjust(sliderName, sliderValue)

### Parameters
- **sliderName** (string) - The name of the shader property to adjust (e.g., 'edgethresh').
- **sliderValue** (float) - The desired value for the shader property (e.g., 0.6).
```

```APIDOC
## shadermatcap

### Description
Set the material capture file for the 'matcap' shader.

### Method
shadermatcap(name)

### Parameters
- **name** (string) - The name of the matcap file to use (e.g., 'mc01').
```

```APIDOC
## shadername

### Description
Choose the rendering shader function.

### Method
shadername(name)

### Parameters
- **name** (string) - The name of the shader to apply (e.g., 'mip' for maximum intensity projection).
```

```APIDOC
## shaderquality1to10

### Description
Set the rendering quality level, balancing speed and visual fidelity.

### Method
shaderquality1to10(i)

### Parameters
- **i** (integer) - The quality level from 1 (fastest) to 10 (highest quality). A value of 6 offers a balance.
```

```APIDOC
## shaderupdategradients

### Description
Recalculate volume properties, often needed after changes to rendering settings.

### Method
shaderupdategradients()
```

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

### Display Modal Message Box

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Shows a message to the user in a dialog box. The script pauses until the user clicks 'OK'.

```python
modalmessage(msg)
```

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

### Tool Panel Visibility

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Control the visibility of the tool panel.

```APIDOC
## toolformvisible

### Description
Show (1) or hide (0) the tool panel.

### Method
toolformvisible(visible)

### Parameters
- **visible** (integer) - 1 to show the tool panel, 0 to hide it.
```

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

### Overlay Interpolation

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Configure the interpolation method for future overlay loading operations.

```APIDOC
## overlayloadsmooth

### Description
Set whether future `overlayload()` calls should use smooth (1) or jagged (0) interpolation.

### Method
overlayloadsmooth(value)

### Parameters
- **value** (integer) - 1 for smooth interpolation, 0 for jagged interpolation.
```

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

### Application Version

Source: https://github.com/rordenlab/mricrogl/blob/master/COMMANDS.md

Retrieve the current version of MRIcroGL.

```APIDOC
## version

### Description
Return the version of MRIcroGL.

### Method
version() -> string
```

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

### View and Rendering Control

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Functions to adjust rendering quality, shaders, and view orientation.

```APIDOC
## bmpzoom

### Description
Changes the resolution of `savebmp()` output.

### Method
`bmpzoom(z)`

### Parameters
- **z** (float) - Zoom factor for bitmap resolution.

## orthoviewmm

### Description
Shows three orthogonal slices of the brain specified in millimeters.

### Method
`orthoviewmm(x, y, z)`

### Parameters
- **x** (float) - X-coordinate in millimeters.
- **y** (float) - Y-coordinate in millimeters.
- **z** (float) - Z-coordinate in millimeters.

## shaderadjust

### Description
Sets the level of a specific shader property.

### Method
`shaderadjust(sliderName, sliderValue)`

### Parameters
- **sliderName** (string) - The name of the shader property to adjust.
- **sliderValue** (float) - The desired value for the property.

## shaderlightazimuthelevation

### Description
Positions the light source that illuminates the rendering.

### Method
`shaderlightazimuthelevation(a, e)`

### Parameters
- **a** (float) - Azimuth angle of the light.
- **e** (float) - Elevation angle of the light.

## shadername

### Description
Chooses the rendering shader function.

### Method
`shadername(name)`

### Parameters
- **name** (string) - The name of the shader function (e.g., 'mip').

## shaderquality1to10

### Description
Sets the rendering quality.

### Method
`shaderquality1to10(i)`

### Parameters
- **i** (int) - Rendering quality level from 1 (fast) to 10 (high quality).

## shaderupdategradients

### Description
Recalculates volume properties for shaders.

### Method
`shaderupdategradients()`

## sharpen

### Description
Applies an unsharp mask to the background volume to enhance edges.

### Method
`sharpen()`

## viewaxial

### Description
Sets the camera position for axial view.

### Method
`viewaxial(SI)`

### Parameters
- **SI** (int) - 1 for superior, 0 for inferior.

## viewcoronal

### Description
Sets the camera position for coronal view.

### Method
`viewcoronal(AP)`

### Parameters
- **AP** (int) - 1 for posterior, 0 for anterior.

## viewsagittal

### Description
Sets the camera position for sagittal view.

### Method
`viewsagittal(LR)`

### Parameters
- **LR** (int) - 1 for left, 0 for right.
```

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

### Remove Haze from Image

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Applies a haze removal algorithm to the image. Requires three parameters.

```python
extract(Otsu,Dil,One)
```

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

### Terminate Application

Source: https://github.com/rordenlab/mricrogl/blob/master/PYTHON.md

Exits the MRIcroGL application. Use with caution as unsaved changes may be lost.

```python
quit()
```