### Config Module Usage Example

Source: https://github.com/pennlinc/qsirecon/blob/main/AGENTS.md

Demonstrates how to read settings from the config module and how to serialize/load configuration to/from disk.

```python
from <pkg> import config

# Read a setting
work_dir = config.execution.work_dir

# Serialize to disk
config.to_filename(path)

# Load from disk (in a subprocess)
config.load(path)
```

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

### Fetch Example BIDS Data

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.interfaces.freesurfer.md

Fetches example BIDS data for testing and sets the current working directory. Requires the niworkflows library.

```python
>>> import os
>>> from niworkflows import data
>>> data_root = data.get_bids_examples(variant='BIDS-examples-1-enh-ds054')
>>> os.chdir(data_root)
```

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

### Running QSIRecon Container with Mounted Volumes

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/contributors.md

Example of running the QSIRecon Docker container, mounting data, output, and the local qsirecon repository. This allows testing changes directly without rebuilding the image.

```bash
$ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
    -v $HOME/projects/qsirecon/qsirecon:/usr/local/miniconda/lib/python3.10/site-packages/qsirecon:ro \
    pennlinc/qsirecon:latest /data /out/out participant \
    -w /out/work/
```

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

### Default Atlases in QSIRecon

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/builtin_workflows.md

Example of how to specify multiple default atlases for a connectivity matrix workflow. Ensure these atlases are available in your QSIRecon installation.

```bash
--atlases 4S156Parcels 4S256Parcels 4S456Parcels Brainnetome246Ext AICHA384Ext Gordon333Ext AAL116
```

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

### Run QSIRecon with Docker

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/installation.md

Execute QSIRecon using a Docker container. Ensure Docker is installed and has sufficient memory allocated (6GB+ for Docker Desktop on macOS). Mount local directories for input data and output, and the Freesurfer license file.

```bash
docker run -ti --rm \
    -v /filepath/to/data/dir \
    -v /filepath/to/output/dir \
    -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
    pennlinc/qsirecon:latest \
    /filepath/to/data/dir /filepath/to/output/dir participant \
    --fs-license-file /opt/freesurfer/license.txt \
    --recon-spec pyafq_tractometry
```

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

### qsirecon.cli.workflow.build_boilerplate

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.cli.workflow.md

Writes boilerplate configuration and setup files within an isolated multiprocessing environment to manage memory scope.

```APIDOC
## qsirecon.cli.workflow.build_boilerplate

### Description
Write boilerplate in an isolated process.

### Method
(Not specified, likely a function call)

### Parameters
- **config_file**: (type not specified) - Description not specified.
- **workflow**: (type not specified) - Description not specified.
```

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

### Installing Non-Python Dependencies in Dockerfile

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/contributors.md

Add non-Python dependencies to the Docker image by including a RUN command in the Dockerfile. This example shows how to install a package using apt-get update and apt-get install.

```dockerfile
RUN apt-get update && \
    apt-get install -y <PACKAGE>
```

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

### qsirecon.utils.sentry.sentry_setup

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.utils.sentry.md

Initializes and sets up the Sentry client for the application.

```APIDOC
## qsirecon.utils.sentry.sentry_setup()

### Description
Sets up the Sentry client for the application. This function should be called during application initialization.
```

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

### qsirecon.workflows.recon.dsi_studio.init_dsi_studio_connectivity_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes the DSI Studio connectivity workflow.

```APIDOC
## init_dsi_studio_connectivity_wf

### Description
Initializes the DSI Studio connectivity workflow.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not applicable.

### Response
Not specified in the source text.
```

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

### Pipeline-level Metadata Example

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/building_workflows.md

Defines the name of the pipeline and lists additional computations based on anatomical images.

```yaml
name: dsistudio_pipeline
anatomical:
- mrtrix_5tt_hsvs
nodes: []
```

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

### qsirecon.workflows.recon.dsi_studio.init_dsi_studio_recon_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes the DSI Studio reconstruction workflow.

```APIDOC
## init_dsi_studio_recon_wf

### Description
Initializes the DSI Studio reconstruction workflow.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not applicable.

### Response
Not specified in the source text.
```

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

### qsirecon.workflows.recon.dsi_studio.init_dsi_studio_autotrack_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes the DSI Studio autotrack workflow.

```APIDOC
## init_dsi_studio_autotrack_wf

### Description
Initializes the DSI Studio autotrack workflow.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not applicable.

### Response
Not specified in the source text.
```

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

### init_qsirecon_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes the main QSIrecon workflow.

```APIDOC
## init_qsirecon_wf

### Description
Initializes the main QSIrecon workflow.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not specified in the source text.

### Response
Not specified in the source text.
```

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

### qsirecon.workflows.recon.dsi_studio.init_dsi_studio_export_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes the DSI Studio export workflow.

```APIDOC
## init_dsi_studio_export_wf

### Description
Initializes the DSI Studio export workflow.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not applicable.

### Response
Not specified in the source text.
```

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

### Mounting Repositories with Docker

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/contributors.md

Use the -v flag with docker run to mount local repositories as source directories within the container for testing without rebuilding the image. Ensure the paths are correct for your local setup.

```bash
-v $HOME/projects/qsirecon/qsirecon:/usr/local/miniconda/lib/python3.10/site-packages/qsirecon:ro
-v $HOME/projects/nipype/nipype:/usr/local/miniconda/lib/python3.10/site-packages/nipype:ro
```

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

### qsirecon.workflows.recon.dsi_studio.init_dsi_studio_autotrack_registration_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes the DSI Studio autotrack registration workflow.

```APIDOC
## init_dsi_studio_autotrack_registration_wf

### Description
Initializes the DSI Studio autotrack registration workflow.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not applicable.

### Response
Not specified in the source text.
```

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

### Add Description to Workflow Object

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/contributors.md

This snippet shows how to add a description to a workflow object using the `__desc__` attribute. The description is formatted using Markdown and can include references to a Bibtex database. Ensure FSL is installed and its version is available.

```python
workflow = Workflow(name=name)
workflow.__desc__ = """\Head-motion parameters with respect to the DWI reference
(transformation matrices, and six corresponding rotation and translation
parameters) are estimated before any spatiotemporal filtering using
`mcflirt` [FSL {fsl_ver}, @mcflirt].
""".format(fsl_ver=fsl.Info().version() or '<ver>')
```

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

### qsirecon.cli.run.main()

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.cli.run.md

The main entry point for the qsirecon command-line interface. This function initiates the q-Space Image reconstruction workflows.

```APIDOC
## qsirecon.cli.run.main()

### Description
Entry point for the q-Space Image reconstruction workflows.

### Signature
main()
```

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

### QSIRecon Architecture Overview

Source: https://github.com/pennlinc/qsirecon/blob/main/AGENTS.md

Illustrates the execution flow from CLI to BIDS-compliant derivative outputs, detailing the roles of CLI, config, workflows, interfaces, utilities, reports, data, and tests.

```text
CLI (parser.py / run.py)
  -> config singleton (config.py, serialized as ToML)
    -> workflow graph construction (workflows/*.py)
      -> Nipype interfaces (interfaces/*.py)
        -> BIDS-compliant derivative outputs
```

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

### qsirecon.workflows.base.init_qsirecon_wf()

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.workflows.base.md

Organizes the execution of QSIrecon, creating a sub-workflow for each subject.

```APIDOC
## qsirecon.workflows.base.init_qsirecon_wf()

### Description
Organizes the execution of QSIrecon, with a sub-workflow for each subject.

### Method
(Not specified, likely a Python function call)

### Endpoint
(Not applicable, Python function)

### Parameters
(None specified)

### Response
(Not specified)
```

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

### qsirecon.workflows.recon.dsi_studio.init_dsi_studio_tractography_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes the DSI Studio tractography workflow.

```APIDOC
## init_dsi_studio_tractography_wf

### Description
Initializes the DSI Studio tractography workflow.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not applicable.

### Response
Not specified in the source text.
```

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

### QSIRecon Command-Line Usage

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/quickstart.md

Displays the full usage information for the QSIRecon command-line interface, including all available arguments and their descriptions.

```bash
usage: qsirecon [-h]
                [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                [--session-id SESSION_ID [SESSION_ID ...]]
                [-d PACKAGE=PATH [PACKAGE=PATH ...]] [--bids-filter-file FILE]
                [--bids-database-dir PATH] [--nprocs NPROCS]
                [--omp-nthreads OMP_NTHREADS] [--mem MEMORY_MB] [--low-mem]
                [--use-plugin FILE] [--sloppy] [--boilerplate-only]
                [--reports-only]
                [--report-output-level {root,subject,session}] [--infant]
                [--b0-threshold B0_THRESHOLD]
                [--output-resolution OUTPUT_RESOLUTION]
                [--fs-license-file PATH] --recon-spec RECON_SPEC
                [--input-type {qsiprep,ukb,hcpya}] [--fs-subjects-dir PATH]
                [--skip-odf-reports]
                [--recon-spec-aux-files RECON_SPEC_AUX_FILES]
                [--atlases ATLAS [ATLAS ...]] [--version] [-v] [-w WORK_DIR]
                [--resource-monitor] [--config-file FILE] [--write-graph]
                [--stop-on-first-crash] [--notrack]
                [--debug {pdb,all} [{pdb,all} ...]]
                input_dir output_dir {participant}
```

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

### qsirecon.utils.sentry.start_ping

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.utils.sentry.md

Initiates a Sentry ping with the provided run UUID and partition number.

```APIDOC
## qsirecon.utils.sentry.start_ping(run_uuid, npart)

### Description
Starts a Sentry ping to indicate activity or status for a given run.

### Parameters
- **run_uuid**: The unique identifier for the run.
- **npart**: The partition number.
```

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

### Build Singularity/Apptainer Image for QSIRecon

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/installation.md

Build a Singularity/Apptainer image from the QSIRecon Docker repository. Replace <version> with the specific version desired. Avoid 'latest' or 'unstable' for production use.

```bash
apptainer build qsirecon-<version>.sif docker://pennlinc/qsirecon:<version>
```

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

### init_pyafq_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.workflows.recon.pyafq.md

Initializes and runs the PyAFQ workflow to generate tract profiles from qsirecon outputs.

```APIDOC
## init_pyafq_wf

### Description
Runs PyAFQ on some qsirecon outputs to generate tract profiles.

### Method
Python Function

### Signature
`qsirecon.workflows.recon.pyafq.init_pyafq_wf(inputs_dict, name='afq', qsirecon_suffix='', params={})`

### Parameters
#### Arguments
- **inputs_dict** (dict) - Dictionary containing qsirecon outputs.
- **name** (str, optional) - Name for the workflow. Defaults to 'afq'.
- **qsirecon_suffix** (str, optional) - Suffix for qsirecon outputs. Defaults to ''.
- **params** (dict, optional) - Parameters for the PyAFQ workflow. Defaults to {}.

### Outputs
- **profiles_csv** (file) - CSV file containing the tract profiles generated by pyAFQ.
```

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

### qsirecon.workflows.recon.dipy.init_dipy_brainsuite_shore_recon_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.workflows.recon.dipy.md

Initializes a Dipy reconstruction workflow using the 3dSHORE method with a Brainsuite-style basis set to reconstruct EAPs and ODFs.

```APIDOC
## qsirecon.workflows.recon.dipy.init_dipy_brainsuite_shore_recon_wf

### Description
Reconstructs EAPs, ODFs, using 3dSHORE (brainsuite-style basis set).

### Method Signature
qsirecon.workflows.recon.dipy.init_dipy_brainsuite_shore_recon_wf(inputs_dict, name='dipy_3dshore_recon', qsirecon_suffix='', params={})

### Parameters
#### Inputs
* **inputs_dict** (*dict*) – Dictionary containing the input node fields.

#### Workflow Parameters
* **name** (*str*) – Name of the workflow. Defaults to 'dipy_3dshore_recon'.
* **qsirecon_suffix** (*str*) – Suffix for the qsirecon outputs. Defaults to ''.
* **params** (*dict*) – Dictionary containing parameters for the reconstruction.
  * **write_fibgz** (bool) - True writes out a DSI Studio fib file.
  * **write_mif** (bool) - True writes out a MRTrix mif file with sh coefficients.
  * **convert_to_multishell** (str) - Either “HCP”, “ABCD”, or “lifespan” to resample the data with the specified scheme.
  * **radial_order** (int) - Radial order for spherical harmonics (even).
  * **zeta** (float) - Zeta parameter for basis set.
  * **tau** (float) - Diffusion parameter. Defaults to 4 * np.pi**2.
  * **regularization** (str) - Either “L2” or “L1”. Defaults to “L2”.
  * **lambdaN** (float) - LambdaN parameter for L2 regularization. Defaults to 1e-8.
  * **lambdaL** (float) - LambdaL parameter for L2 regularization. Defaults to 1e-8.
  * **regularization_weighting** (int or "CV") - L1 regularization weighting. Defaults to “CV” (use cross-validation). Can specify a static value.
  * **l1_positive_constraint** (bool) - Use positivity constraint.
  * **l1_maxiter** (int) - Maximum number of iterations for L1 optimization. Defaults to 1000.
  * **l1_alpha** (float) - Alpha parameter for L1 optimization. Defaults to 1.0.
  * **pos_grid** (int) - Grid points for estimating EAP. Defaults to 11.
  * **pos_radius** (float) - Radius for EAP estimation. Defaults to 20e-03.

### Outputs
* **shore_coeffs** (*str*) – Path to the 3dSHORE coefficients.
* **rtop** (*str*) – Path to the Voxelwise Return-to-origin probability.
* **rtap** (*str*) – Path to the Voxelwise Return-to-axis probability.
* **rtpp** (*str*) – Path to the Voxelwise Return-to-plane probability.
```

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

### Building a Local QSIRecon Docker Image

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/contributors.md

Build a local Docker image named 'qsirecon' from within your working QSIRecon repository directory. This image can then be used in docker commands by replacing the official image name.

```bash
~/projects/qsirecon$ docker build -t qsirecon .
```

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

### init_dsi_studio_autotrack_registration_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.workflows.recon.dsi_studio.md

Runs DSI Studio's AutoTrack method to create a map.gz file without saving bundles. This is useful for workflows requiring both fib and map files, leveraging GQI scalars for better registration.

```APIDOC
## qsirecon.workflows.recon.dsi_studio.init_dsi_studio_autotrack_registration_wf

### Description
Run DSI Studio’s AutoTrack method to create a map.gz file. No bundles are saved. This workflow is designed to be used as input to other workflows that need both a fib and a map file (eg FOD Autotrack). The registration is better using GQI scalars than the imported FOD scalars.

### Inputs
- **fibgz** (file): A DSI Studio fib file produced by DSI Studio reconstruction.

### Outputs
- **fibgz** (file): The input fibgz file, unaltered.
- **fibgz_map** (file): A map.gz file corresponding to the fibgz file.
```

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

### init_test_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes a test workflow.

```APIDOC
## init_test_wf

### Description
Initializes a test workflow.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not specified in the source text.

### Response
Not specified in the source text.
```

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

### qsirecon.cli.workflow.build_workflow

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.cli.workflow.md

Creates the Nipype Workflow, which represents the entire execution graph for data processing.

```APIDOC
## qsirecon.cli.workflow.build_workflow

### Description
Create the Nipype Workflow that supports the whole execution graph.

### Method
(Not specified, likely a function call)

### Parameters
- **config_file**: (type not specified) - Description not specified.
- **retval**: (type not specified) - Description not specified.
```

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

### qsirecon.workflows.recon.build_workflow.init_dwi_recon_workflow

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes the DWI (Diffusion Weighted Imaging) reconstruction workflow.

```APIDOC
## init_dwi_recon_workflow

### Description
Initializes the DWI (Diffusion Weighted Imaging) reconstruction workflow.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not applicable.

### Response
Not specified in the source text.
```

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

### qsirecon.workflows.recon.anatomical.init_register_fs_to_qsiprep_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes the workflow for registering FreeSurfer (FS) data to qsiprep.

```APIDOC
## init_register_fs_to_qsiprep_wf

### Description
Initializes the workflow for registering FreeSurfer (FS) data to qsiprep.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not applicable.

### Response
Not specified in the source text.
```

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

### build_documentation Function

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.utils.boilerplate.md

Builds documentation for a given Nipype interface, focusing on inputs specified during initialization.

```APIDOC
### qsirecon.utils.boilerplate.build_documentation(interface)

#### Description
Build documentation for a given interface. This is only useful for inputs that are specified when the interface is initialized. It will not work for inputs that are set through workflow connections. It will work with either the original interface object or a Nipype Node. It has not been tested with MapNodes or JoinNodes.
```

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

### init_pyafq_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes a workflow for PyAFQ tractometry and visualization.

```APIDOC
## init_pyafq_wf

### Description
Initializes a workflow for PyAFQ tractometry and visualization.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not specified in the source text.

### Response
Not specified in the source text.
```

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

### init_qsirecon_to_fsl_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.workflows.recon.converters.md

Converts QSIRecon outputs (images, bval, bvec) to FSL standard orientation.

```APIDOC
## init_qsirecon_to_fsl_wf

### Description
Converts QSIRecon outputs (images, bval, bvec) to FSL standard orientation.

### Method
Not specified (likely a Python function call)

### Parameters
- **inputs_dict** (dict) - Required - Dictionary containing input files.
- **name** (string) - Optional - Defaults to 'qsirecon_to_fsl'.
- **qsirecon_suffix** (string) - Optional - Defaults to ''.
- **params** (dict) - Optional - Defaults to {}.

### Inputs
(Not explicitly defined in source, likely inferred from workflow)

### Outputs
(Not explicitly defined in source, likely inferred from workflow)
```

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

### Run QSIRecon with Apptainer

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/quickstart.md

This command executes the QSIRecon workflow using Apptainer, specifying input and output directories, participant mode, working directory, number of threads, and the reconstruction specification.

```bash
apptainer run \
    --containall \
    --writable-tmpfs \
    -B "${PWD}" \
    qsirecon-latest.sif \
    "${PWD}/inputs/qsiprep" \
    "${PWD}/results/qsirecon" \
    participant \
    -w "${PWD}/work" \
    --nthreads 8 \
    --omp-nthreads 8 \
    --recon-spec dsi_studio_autotrack \
    -v -v
```

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

### init_json_preproc_report_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes a workflow to generate a JSON preprocessing report.

```APIDOC
## init_json_preproc_report_wf

### Description
Initializes a workflow to generate a JSON preprocessing report.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not specified in the source text.

### Response
Not specified in the source text.
```

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

### QSIRecon Atlas Directory Structure

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/builtin_workflows.md

Illustrates the expected directory structure for atlases within the QSIRecon project, including dataset description and atlas files.

```bash
qsirecon/
   atlases/
      dataset_description.json
      atlas-<label>/
         atlas-<label>_space-<label>_res-<label>_dseg.nii.gz
         atlas-<label>_space-<label>_res-<label>_dseg.json
         atlas-<label>_dseg.tsv
```

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

### Run QSIPrep with FreeSurfer Data

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/input_data.md

Execute QSIPrep reconstruction, specifying the directory containing FreeSurfer outputs using the --fs-subjects-dir flag. Ensure the FreeSurfer license is accessible.

```bash
apptainer run \
    --containall \
    --writable-tmpfs \
    -B "${PWD}" \
    -B "${FREESURFER_HOME}/license.txt":/license.txt \
    "${PWD}/derivatives/qsiprep" \
    "${PWD}/derivatives/qsirecon" \
    participant \
    -w "${PWD}/work" \
    --nthreads 8 \
    --omp-nthreads 8 \
    --fs-license-file /license.txt \
    --recon-spec mrtrix_multishell_msmt_ACT-hsvs \
    --fs-subjects-dir "${PWD}/derivatives/freesurfer" \
    -v -v
```

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

### init_mrtrix_connectivity_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes a workflow for MRtrix-based connectivity analysis.

```APIDOC
## init_mrtrix_connectivity_wf

### Description
Initializes a workflow for MRtrix-based connectivity analysis.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not specified in the source text.

### Response
Not specified in the source text.
```

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

### qsirecon.workflows.recon.converters.init_qsirecon_to_fsl_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Initializes a workflow to convert qsirecon output to FSL (FMRIB Software Library) format.

```APIDOC
## init_qsirecon_to_fsl_wf

### Description
Initializes a workflow to convert qsirecon output to FSL (FMRIB Software Library) format.

### Method
Not specified (likely a Python function call)

### Endpoint
Not applicable (Python function)

### Parameters
Not specified in the source text.

### Request Example
Not applicable.

### Response
Not specified in the source text.
```

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

### init_fibgz_to_mif_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.workflows.recon.converters.md

Initializes a workflow to convert DSI Studio fibgz files to MRTrix mif format. This function requires further documentation.

```APIDOC
## init_fibgz_to_mif_wf

### Description
Initializes a workflow to convert DSI Studio fibgz files to MRTrix mif format. This function requires further documentation.

### Method
Not specified (likely a Python function call)

### Parameters
- **name** (string) - Optional - Defaults to 'fibgz_to_mif'.
- **qsirecon_suffix** (string) - Optional - Defaults to ''.
- **params** (dict) - Optional - Defaults to {}.

### Inputs
(Not explicitly defined in source, likely inferred from workflow)

### Outputs
(Not explicitly defined in source, likely inferred from workflow)
```

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

### init_test_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.workflows.recon.utils.md

Initializes a testing workflow for the qsirecon pipeline. This function is designed to simulate the saving of derivatives and test the pipeline's output structure, particularly useful during development or for validation purposes.

```APIDOC
## init_test_wf

### Description
Initializes a workflow specifically for testing purposes, simulating how derivatives will be saved by the qsirecon pipeline. It helps in verifying the output structure and naming conventions.

### Signature
`init_test_wf(inputs_dict, name='test_wf', qsirecon_suffix='test', params={})`

### Parameters
- **inputs_dict** (dict) - Dictionary containing input data and parameters for the test.
- **name** (str, optional) - The name for the workflow. Defaults to 'test_wf'.
- **qsirecon_suffix** (str, optional) - Suffix to append to reconstructed outputs during testing. Defaults to 'test'.
- **params** (dict, optional) - Additional parameters for the test workflow. Defaults to an empty dictionary.
```

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

### DSIStudioCreateSrc

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api_reference.md

Creates a source file using DSI Studio.

```APIDOC
## DSIStudioCreateSrc

### Description
Creates a source file using DSI Studio.

### Method
Not specified (likely a function call within a Python SDK).

### Endpoint
Not applicable (SDK function).

### Parameters
Not specified in the source text.

### Request Example
Not specified in the source text.

### Response
Not specified in the source text.
```

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

### init_scalar_to_bundle_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.workflows.recon.scalar_mapping.md

Initializes a workflow to map scalar images to bundles. It generates summary statistics in tsv format for each bundle.

```APIDOC
## init_scalar_to_bundle_wf

### Description
Map scalar images to bundles. Generates summary statistics in tsv format.

### Parameters
#### Inputs
- **tck_files** (List[str]) - MRtrix3 format tck files for each bundle.
- **bundle_names** (List[str]) - Names that describe which bundles are present in tck_files.
- **recon_scalars** (List[dict]) - List of dictionaries containing scalar info.

### Outputs
#### bundle_summaries
- (tsv) - Summary statistics in tsv format.
```

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

### Run QSIRecon with Singularity/Apptainer

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/installation.md

Execute QSIRecon using a Singularity/Apptainer image. Bind local directories for input/output and the Freesurfer license. This command uses specific recon specs and verbose output flags.

```bash
apptainer run \
    --containall \
    --writable-tmpfs \
    -B "${PWD}","${FREESURFER_HOME}"/license.txt:/opt/freesurfer/license.txt \
    qsirecon-<version>.sif \
    "${PWD}"/derivatives/qsiprep \
    "${PWD}"/derivatives/qsirecon \
    participant \
    --fs-license-file /opt/freesurfer/license.txt \
    --recon-spec ss3t_autotrack \
    -w "${PWD}/work" \
    -v -v
```

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

### init_dsi_studio_recon_wf

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.workflows.recon.dsi_studio.md

Reconstructs diffusion data using DSI Studio, creating a .src.gz file from input DWI, bvals, and bvecs, and then reconstructing ODFs using GQI.

```APIDOC
## init_dsi_studio_recon_wf

### Description
Reconstructs diffusion data using DSI Studio. This workflow creates a `.src.gz` file from the input dwi, bvals and bvecs, then reconstructs ODFs using GQI.

### Method
Python Function

### Parameters
#### Inputs
- **Default qsirecon inputs** (dict) - Requires standard qsirecon inputs like dwi, bvals, bvecs.

#### Parameters (Params)
- **ratio_of_mean_diffusion_distance** (float) - Default 1.25. Distance to sample EAP at.

### Outputs
- **fibgz** (file) - A DSI Studio fib file containing GQI ODFs, peaks and scalar values.

### Request Example
```python
init_dsi_studio_recon_wf(inputs_dict={'dwi': '/path/to/dwi.nii.gz', 'bvals': '/path/to/bvals', 'bvecs': '/path/to/bvecs'},
                         params={'ratio_of_mean_diffusion_distance': 1.25})
```

### Response
#### Success Response
- **fibgz** (file) - Path to the generated DSI Studio fib.gz file.
```

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

### Running QSIRecon Container with Bash Entrypoint

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/contributors.md

Access the QSIRecon Docker container's bash shell by specifying --entrypoint=bash. This is useful for interactive work within the container environment, with mounted volumes for data and code.

```bash
$ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
    -v $HOME/projects/qsirecon/qsirecon:/usr/local/miniconda/lib/python3.10/site-packages/qsirecon:ro --entrypoint=bash \
    pennlinc/qsirecon:latest
```

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

### qsirecon.interfaces.converters.popen_run

Source: https://github.com/pennlinc/qsirecon/blob/main/docs/api/qsirecon.interfaces.converters.md

Runs a command using subprocess.Popen.

```APIDOC
## qsirecon.interfaces.converters.popen_run(arg_list)

Runs a command using subprocess.Popen.

### Parameters:

arg_list (list) - A list of strings representing the command and its arguments.
```