### setup()

Source: https://brainsuite.org/bstr/apidocs/reference/setup.html

Configures the BrainSuite installation path by reading and writing to the bstr.ini file.

```APIDOC
## setup()

### Description
Reads from and writes to the setup configuration file (bstr.ini) for bstr. This is usually called automatically upon package installation but can be executed manually.

### Parameters
#### Arguments
- **brainsuite_path** (string) - Optional - Path to the BrainSuite installation.
- **quiet** (logical) - Optional - If FALSE, displays messages to the user.
- **raise_error** (logical) - Optional - If TRUE, stops execution if the file does not exist. Defaults to FALSE.
```

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

### Verify bstr installation

Source: https://brainsuite.org/bstr/installation.html

Load the library and check the BrainSuite installation path to confirm successful setup.

```R
library(bstr)
```

```R
get_brainsuite_install_path()
```

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

### Install bstr Locally on Windows (Forward Slash)

Source: https://brainsuite.org/bstr/apidocs/index.html

Install bstr from a local .tar.gz file on Windows using forward slashes in the path. Replace 'C:/path/to/' with the actual directory. Ensure 'devtools' is installed first.

```r
install.packages('devtools')
devtools::install_local('C:/path/to/bstr_0.5.2.tar.gz')
```

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

### Install bstr Locally on Windows (Double Backslash)

Source: https://brainsuite.org/bstr/apidocs/index.html

Install bstr from a local .tar.gz file on Windows using double backslashes in the path. Replace 'C:\path\to\' with the actual directory. Ensure 'devtools' is installed first.

```r
install.packages('devtools')
devtools::install_local('C:\\path\\to\\bstr_0.5.2.tar.gz')
```

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

### Install bstr Locally on Mac/Linux

Source: https://brainsuite.org/bstr/apidocs/index.html

Install bstr from a local .tar.gz file on macOS or Linux. Replace '/path/to/' with the actual directory where the file was downloaded. Ensure 'devtools' is installed first.

```r
install.packages('devtools')
devtools::install_local('/path/to/bstr_0.5.2.tar.gz')
```

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

### Install Graphviz (Optional)

Source: https://brainsuite.org/nipype_installation

Install Graphviz and its development headers, which are optional dependencies for Nipype. This step requires sudo privileges.

```bash
sudo apt-get install graphviz libgraphviz-dev
```

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

### Call the setup function for bstr

Source: https://brainsuite.org/bstr/apidocs/reference/setup.html

This function is used to set up the bstr package. It can optionally take a path to the BrainSuite installation and control message display and error handling.

```R
setup(brainsuite_path = NULL, quiet = FALSE, raise_error = TRUE)
```

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

### Install bstr via URL

Source: https://brainsuite.org/bstr/apidocs/index.html

Use this command to install bstr version 0.5.2 directly from the BrainSuite server. Ensure 'devtools' is installed first.

```r
install.packages('devtools')
devtools::install_url('http://brainsuite.org/wp-content/uploads/2024/09/bstr_0.5.2.tar.gz')
```

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

### Build and Install Cortical Extraction Tools

Source: https://brainsuite.org/building

Run the build script to compile libraries and routines, optionally installing them to the home directory.

```bash
./buildall.sh
```

```bash
./buildall.sh install
```

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

### Install bstr from local folder on Windows

Source: https://brainsuite.org/bstr/installation.html

Install the package from a local file path on Windows, using either double backslashes or forward slashes.

```R
install.packages('devtools')
devtools::install_local('C:\\path\\to\\bstr_0.5.2.tar.gz')
```

```R
install.packages('devtools')
devtools::install_local('C:/path/to/bstr_0.5.2.tar.gz')
```

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

### Verify BrainSuite Installation

Source: https://brainsuite.org/nipype_installation

After adding BrainSuite to your PATH, run the 'bse' command in the terminal. If instruction text appears, the installation and PATH configuration are successful.

```bash
bse
```

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

### Run BDP with Default Settings

Source: https://brainsuite.org/processing/diffusion/pipeline

Example command to execute BDP with default settings on Windows.

```bash
bdp.exe C:\Users\name\subject\diffusion_processing\subj1.bfc.nii.gz
 --nii C:\Users\name\subject\diffusion_processing\subj1.dwi.nii.gz
 -g C:\Users\name\subject\diffusion_processing\subj1.bvec 
 -b C:\Users\name\subject\diffusion_processing\subj1.bval
```

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

### BDP Input File List

Source: https://brainsuite.org/processing/diffusion/pipeline

Example file structure for BDP processing inputs.

```text
C:\Users\name\subject\diffusion_processing\subj1.bfc.nii.gz
C:\Users\name\subject\diffusion_processing\subj1.dwi.nii.gz
C:\Users\name\subject\diffusion_processing\subj1.bvec
C:\Users\name\subject\diffusion_processing\subj1.bval
```

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

### Verify Anaconda Installation

Source: https://brainsuite.org/nipype_installation

Open a Python session by running 'python' in the terminal. If Anaconda is correctly installed and in your PATH, 'Anaconda' will appear in the header text.

```python
python
```

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

### Example: Load SBA Data

Source: https://brainsuite.org/bstr/apidocs/reference/load_bstr_data.html

Example of loading surface-based analysis (SBA) data. Specify the subject directory, demographic CSV file, and hemisphere. Smoothing can also be applied.

```R
my_sba_data <- load_bstr_data(type="sba", subjdir = "/path/to/my/subjectdirectory",
csv = "/path/to/my/demographics.csv", hemi = "left", smooth = 2.5)
```

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

### Test Nipype BrainSuite Interface Installation

Source: https://brainsuite.org/nipype_installation

Open a Python session and attempt to import the brainsuite interface from nipype.interfaces. This import should run without errors if the installation was successful.

```python
python
from nipype.interfaces import brainsuite
```

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

### Example Usage of load_bstr_data_from_filelist

Source: https://brainsuite.org/bstr/apidocs/reference/load_bstr_data_from_filelist.html

Example of how to use the load_bstr_data_from_filelist function with specified paths for CSV, atlas, and mask file. The 'type' and 'file_col' arguments are also set.

```R
if (FALSE) {
my_data <- load_bstr_data_from_filelist(
 csv = "/path/to/my/demographics.csv",
 type="sba",
 file_col = "COL_NAME",
 atlast = "/path/to/atlas",
 maskfile = "/path/to/maskfile")
}
```

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

### Run pialmesh via command line

Source: https://brainsuite.org/processing/surfaceextraction/pial

Example command for executing the pialmesh tool with required input, output, fraction, and mask files.

```bash
pialmesh -i input_mesh.dfs -o output_mesh.dfs -f frac_file.nii.gz -m mask_file.nii.gz
```

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

### GET /get_brainsuite_path_from_bstr_ini

Source: https://brainsuite.org/bstr/apidocs/reference/get_brainsuite_path_from_bstr_ini.html

Retrieves the BrainSuite installation path directly from the bstr.ini configuration file.

```APIDOC
## GET /get_brainsuite_path_from_bstr_ini

### Description
Retrieves the BrainSuite installation path from the bstr.ini configuration file.

### Method
GET

### Endpoint
/get_brainsuite_path_from_bstr_ini
```

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

### GET /get_brainsuite_install_path

Source: https://brainsuite.org/bstr/apidocs/reference/get_brainsuite_install_path.html

Retrieves the installation path for BrainSuite with options to control warning messages and error handling.

```APIDOC
## GET /get_brainsuite_install_path

### Description
Retrieve the BrainSuite installation path.

### Method
GET

### Endpoint
/get_brainsuite_install_path

### Parameters
#### Query Parameters
- **quiet** (boolean) - Optional - Specifies whether warnings/messages should be displayed.
- **raise_error** (boolean) - Optional - Specifies whether an exception should be raised.
```

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

### Navigate to Data Directory

Source: https://brainsuite.org/tutorials/dtiexercise

Change the current working directory to the location of the tutorial files.

```shell
cd C:\Users\Joe\Downloads\BrainSuiteTutorialDWI
```

```shell
cd /Users/Joe/Downloads/BrainSuiteTutorialDWI
```

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

### Verify BrainSuite Installation Path

Source: https://brainsuite.org/bstr/apidocs/index.html

This function checks and displays the installation path of BrainSuite. It is used to verify that bstr can locate the BrainSuite installation.

```r
get_brainsuite_install_path()
```

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

### Acquire Tutorial Data via Bash

Source: https://brainsuite.org/nipype-cse

Commands to download and extract the BrainSuite Nipype tutorial dataset into the user's Documents directory.

```bash
curl http://users.bmap.ucla.edu/~jwong/BrainSuiteNipype_Tutorial.zip -o "BrainSuiteNipype_Tutorial.zip"  
unzip -o -qq BrainSuiteNipype_Tutorial.zip -d ~/Documents
```

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

### Install Nipype Developer Version

Source: https://brainsuite.org/nipype_installation

Navigate to the site-packages directory within your Anaconda installation and clone the Nipype repository. Then, install its requirements and develop the package.

```bash
cd ~/anaconda*/lib/python*/site-packages/ 
git clone https://github.com/nipy/nipype.git 
cd nipype 
pip install -r requirements.txt 
python setup.py develop
```

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

### Clone Sample Data Repository

Source: https://brainsuite.org/BIDS/walkthrough.html

Clone the GitHub repository to download the sample data required for the walk-through demo. This method downloads approximately 776MB of data.

```bash
git clone https://github.com/BrainSuite/BrainSuiteBIDSAppSampleData.git

```

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

### Install rmarkdown package

Source: https://brainsuite.org/bstr/reproducepaper.html

Install the rmarkdown package in the R console if it is not already available.

```R
install.packages("rmarkdown")
```

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

### Validate BrainSuite installation path

Source: https://brainsuite.org/bstr/apidocs/reference/is_valid_brainsute_install_path.html

Use this function to verify if the provided string is a valid path to a BrainSuite installation.

```R
is_valid_brainsute_install_path(brainsuite_path = "")
```

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

### Run BFP Binary from Bash

Source: https://brainsuite.org/bfp

Execute the BFP tool using its bash script. Provide the configuration file, input NIfTI files, study name, subject ID, and session ID as arguments.

```bash
bfp.sh /home/ajoshi/bfp/supp_data/config.ini /home/ajoshi/sub-01_T1w.nii.gz /home/ajoshi/sub-01_rest.nii.gz /home/ajoshi/mystudy sub-01 rest 2
```

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

### Set BrainSuite Installation Path in bstr.ini

Source: https://brainsuite.org/bstr/apidocs/reference/set_brainsuite_path_in_bstr_ini.html

Use this function to specify the directory where BrainSuite is installed. The `brainsuite_path` argument is required.

```R
set_brainsuite_path_in_bstr_ini(brainsuite_path)
```

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

### Retrieve BrainSuite installation path

Source: https://brainsuite.org/bstr/apidocs/reference/get_brainsuite_path_from_bstr_ini.html

Call this function to programmatically determine the BrainSuite installation directory based on the bstr.ini file.

```R
get_brainsuite_path_from_bstr_ini()
```

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

### Build Docker Image from Source

Source: https://brainsuite.org/BIDS/installation.html

Clone the repository and build the Docker image locally. Note that this is not recommended due to dependencies on third-party repositories.

```bash
git clone https://github.com/bids-apps/BrainSuite.git
cd BrainSuite
docker build -t brainsuite .
```

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

### Initialize BstrRmdVolumeOutput

Source: https://brainsuite.org/bstr/apidocs/reference/BstrRmdVolumeOutput.html

Constructor for the BstrRmdVolumeOutput class. Sets the output directory.

```R
BstrRmdVolumeOutput$new(outdir = "./")
```

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

### Check BrainSuite Installation Status

Source: https://brainsuite.org/bstr/apidocs/reference/is_brainsute_installed.html

Use this function to confirm that BrainSuite is installed and its configuration is valid. It checks for the existence of required atlas files and data by parsing the `bstr.ini` file. Set `quiet` to TRUE to suppress messages and `raise_error` to TRUE to throw an exception if the installation is invalid.

```R
is_brainsute_installed(quiet = FALSE, raise_error = FALSE)
```

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

### Example svreg_make_atlas Execution (Mac/Linux)

Source: https://brainsuite.org/processing/svreg/creating-custom-atlases

This command shows how to execute svreg_make_atlas on Mac or Linux systems, providing the subject's file prefix and the atlas directory path, along with the -E flag for manually edited volumetric labels.

```bash
./svreg_make_atlas.sh ~/Documents/CustomAtlas/subj1 /Applications/BrainSuite16a1/svreg/BCI-DNI_brain_atlas/BCI-DNI_brain -E
```

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

### Example svreg_make_atlas Execution (Windows)

Source: https://brainsuite.org/processing/svreg/creating-custom-atlases

This command illustrates how to run the svreg_make_atlas module on Windows, specifying the paths for the subject's data and the base atlas, and including the -E flag for edited labels.

```bash
svreg_make_atlas.exe C:\Users\BrainSuiteUser\Documents\CustomAtlas\subj1 C:\Program Files\BrainSuite16a1\svreg\BCI-DNI_brain_atlas\BCI-DNI_brain -E
```

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

### Get Color Palette Function Signature

Source: https://brainsuite.org/bstr/apidocs/reference/get_color_palette.html

Call this function with the name of the colormap and the desired number of colors to get a hex color code list.

```R
get_color_palette(cmap_name, N)
```

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

### Launch BrainSuite Dashboard with Singularity

Source: https://brainsuite.org/BIDS/dashboard.html

Starts the dashboard monitoring using Singularity, utilizing local host file system paths directly.

```bash
singularity run bids_brainsuite_v23a.simg \
      /path/to/local/input /path/to/local/output participant \
      --stages DASHBOARD --localWebserver
```

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

### Launch BrainSuite Dashboard with Docker

Source: https://brainsuite.org/BIDS/dashboard.html

Starts a local web server for the dashboard using Docker, exposing port 9095 to the host.

```bash
docker run -ti --rm \
  -p 9095:9095
  -v /path/to/local/bids/input/dataset/:/data:ro \
  -v /path/to/local/output/:/output \
  bids/brainsuite:v23a \
  /data /output participant --stages DASHBOARD --localWebserver
```

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

### Initialize BstrRmdRoiOutput

Source: https://brainsuite.org/bstr/apidocs/reference/BstrRmdRoiOutput.html

Constructor for the BstrRmdRoiOutput class. Use this to create a new instance, optionally specifying an output directory.

```R
BstrRmdRoiOutput$new(outdir = NULL)
```

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

### Retrieve BrainSuite installation path

Source: https://brainsuite.org/bstr/apidocs/reference/get_brainsuite_install_path.html

Use this function to locate the BrainSuite installation directory. Set quiet to TRUE to suppress messages and raise_error to FALSE to prevent exceptions.

```R
get_brainsuite_install_path(quiet = TRUE, raise_error = FALSE)
```

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

### Initialize BstrRmdOutput

Source: https://brainsuite.org/bstr/apidocs/reference/BstrRmdOutput.html

Creates a new instance of the BstrRmdOutput class.

```R
BstrRmdOutput$new(outdir = NULL)
```

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

### Check BrainSuite Installation

Source: https://brainsuite.org/bstr/apidocs/reference/is_brainsute_installed.html

Verifies the BrainSuite installation by checking for necessary atlas files, data, and valid paths in the bstr.ini configuration file. This function is typically called during package loading.

```APIDOC
## is_brainsute_installed

### Description
Check if the BrainSuite installation is valid by verifying if the appropriate atlas files and data exist. This function is called from `.onLoad()` when the package is loaded. It opens `bstr.ini` and checks if all the paths are valid.

### Method
NA (This appears to be an R function, not a typical REST API endpoint)

### Endpoint
NA

### Parameters
#### Arguments 
- **quiet** (boolean) - Optional - specifying whether warnings/messages should be displayed 
- **raise_error** (boolean) - Optional - specifying whether an exception should be raised

### Request Example
NA

### Response
NA (This function likely returns a boolean or raises an error based on the installation status.)
```

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

### Singularity Bind Mount Option

Source: https://brainsuite.org/BIDS/group-level.html

If your Singularity image cannot access local files, append the `--bind` argument with the relevant folder path to the `singularity run` command.

```bash
--bind /path/to/folder
```

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

### Add Anaconda to System Path

Source: https://brainsuite.org/nipype_installation

Add Anaconda's bin directory to your system's PATH. This can be done during Anaconda installation or by editing your .bashrc file. Adjust 'anaconda2' or 'anaconda3' based on your installation.

```bash
export PATH=/home/user/anaconda2/bin:$PATH
```

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

### Run BDP for ODF and Tensor Estimation

Source: https://brainsuite.org/processing/diffusion/pipeline

Example command to execute BDP with specific flags for ODF and tensor estimation.

```bash
bdp.exe C:\Users\name\subject\diffusion_processing\subj1.bfc.nii.gz --FRT --FRACT --tensor
 --nii C:\Users\name\subject\diffusion_processing\subj1.dwi.nii.gz
 -g C:\Users\name\subject\diffusion_processing\subj1.bvec
```

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

### Launch BrainSuite Dashboard for AOMIC-PIOP1 (Local Web Server)

Source: https://brainsuite.org/BIDS/paperoutput.html

Launch the BrainSuite Dashboard for AOMIC-PIOP1 processing by starting a local web server. This command is used when the institution does not have a pre-existing web server.

```bash
singularity run $BRAINSUITEBIDSAPP $AOMIC_PIOP1_INPUT $AOMIC_PIOP1_OUTPUT participant \
    --QCdir $QCDIR_AOMIC_PIOP1 --stages DASHBOARD --localWebserver

```

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

### Example: Load ROI Data

Source: https://brainsuite.org/bstr/apidocs/reference/load_bstr_data.html

Example of loading region of interest (ROI) data. Specify the subject directory, demographic CSV file, ROI IDs, and the desired ROI measure (e.g., 'gmthickness').

```R
my_roi_data <- load_bstr_data(type="roi", subjdir = "/path/to/my/subjectdirectory",
csv="/path/to/my/demographics.csv", roiids=501, roimeas="gmthickness")
```

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

### set_brainsuite_path_in_bstr_ini

Source: https://brainsuite.org/bstr/apidocs/reference/set_brainsuite_path_in_bstr_ini.html

Sets the BrainSuite installation path in the bstr.ini configuration file.

```APIDOC
## set_brainsuite_path_in_bstr_ini

### Description
Sets the BrainSuite installation path in the bstr.ini configuration file.

### Parameters
#### Arguments
- **brainsuite_path** (string) - Required - Path to the BrainSuite installation

### Request Example
set_brainsuite_path_in_bstr_ini("/path/to/brainsuite")
```