QSIRecon

https://qsirecon.readthedocs.io/en/latest/
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QSIRecon is a diffusion MRI reconstruction pipeline that builds post-processing workflows for...
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### Fetch Example BIDS Data

Source: https://qsirecon.readthedocs.io/en/latest/api/qsirecon.interfaces.freesurfer.html

Fetches example BIDS data for testing and demonstration purposes. Changes the current working directory to the root of the fetched data.

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

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

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

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the DSI Studio connectivity workflow.

```APIDOC
## init_dsi_studio_connectivity_wf

### Description
Initializes the DSI Studio connectivity workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### Installing Non-Python Dependencies in Dockerfile

Source: https://qsirecon.readthedocs.io/en/latest/_sources/contributors.rst.txt

Install non-Python dependencies within the Docker image using a RUN command in the Dockerfile. This example shows how to install an apt package.

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

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

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

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the DSI Studio reconstruction workflow.

```APIDOC
## init_dsi_studio_recon_wf

### Description
Initializes the DSI Studio reconstruction workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### Get Template Files

Source: https://qsirecon.readthedocs.io/en/latest/api/qsirecon.interfaces.anatomical.html

Retrieves a specified template file and its corresponding mask. Useful for aligning or comparing diffusion data to a standard space.

```python
from qsirecon.interfaces.anatomical import GetTemplate

get_template = GetTemplate()
get_template.inputs.template_name = 'MNI152NLin2009cAsym'
get_template.run()
```

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

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

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the DSI Studio autotrack workflow.

```APIDOC
## init_dsi_studio_autotrack_wf

### Description
Initializes the DSI Studio autotrack workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### qsirecon.workflows.base.init_qsirecon_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the main QSIrecon workflow.

```APIDOC
## init_qsirecon_wf

### Description
Initializes the main QSIrecon workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### Interactive Bash Session in Docker Container

Source: https://qsirecon.readthedocs.io/en/latest/_sources/contributors.rst.txt

Start an interactive bash session within the QSIRecon Docker container, mounting local directories. This is useful for development and debugging.

```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
```

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

### Run QSIRecon with Docker

Source: https://qsirecon.readthedocs.io/en/latest/_sources/installation.rst.txt

Use this command to run QSIRecon within a Docker container. Ensure Docker is installed and volumes for data, output, and the FreeSurfer license are correctly mapped.

```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.workflows.recon.dsi_studio.init_dsi_studio_export_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the DSI Studio export workflow.

```APIDOC
## init_dsi_studio_export_wf

### Description
Initializes the DSI Studio export workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### qsirecon.workflows.recon.mrtrix.init_mrtrix_connectivity_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the MRTrix connectivity workflow.

```APIDOC
## init_mrtrix_connectivity_wf

### Description
Initializes the MRTrix connectivity workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### QSIRecon TORTOISE Reconstruction Derivatives

Source: https://qsirecon.readthedocs.io/en/latest/outputs.html

Example output structure for the TORTOISE reconstruction method, showing dataset description, HTML reports, logs, and DWI-specific parameter maps.

```plaintext
qsirecon/
   derivatives/
      qsirecon-TORTOISE/
         dataset_description.json
         sub-<label>[_ses-<label>].html
         logs/
         sub-<label>/[ses-<label>/]
            figures/
            dwi/
               <source_entities>_model-mapmri_param-ng_dwimap.json
               <source_entities>_model-mapmri_param-ng_dwimap.nii.gz
               <source_entities>_model-mapmri_param-ngpar_dwimap.json
               <source_entities>_model-mapmri_param-ngpar_dwimap.nii.gz
               <source_entities>_model-mapmri_param-ngperp_dwimap.json
               <source_entities>_model-mapmri_param-ngperp_dwimap.nii.gz
               <source_entities>_model-mapmri_param-pa_dwimap.json
               <source_entities>_model-mapmri_param-pa_dwimap.nii.gz
               <source_entities>_model-mapmri_param-path_dwimap.json
               <source_entities>_model-mapmri_param-path_dwimap.nii.gz
               <source_entities>_model-mapmri_param-rtap_dwimap.json
               <source_entities>_model-mapmri_param-rtap_dwimap.nii.gz
               <source_entities>_model-mapmri_param-rtop_dwimap.json
               <source_entities>_model-mapmri_param-rtop_dwimap.nii.gz
               <source_entities>_model-mapmri_param-rtpp_dwimap.json
               <source_entities>_model-mapmri_param-rtpp_dwimap.nii.gz
               <source_entities>_model-tensor_param-ad_dwimap.json
               <source_entities>_model-tensor_param-ad_dwimap.nii.gz
               <source_entities>_model-tensor_param-am_dwimap.json
               <source_entities>_model-tensor_param-am_dwimap.nii.gz
               <source_entities>_model-tensor_param-fa_dwimap.json
               <source_entities>_model-tensor_param-fa_dwimap.nii.gz
               <source_entities>_model-tensor_param-li_dwimap.json
               <source_entities>_model-tensor_param-li_dwimap.nii.gz
               <source_entities>_model-tensor_param-rd_dwimap.json
               <source_entities>_model-tensor_param-rd_dwimap.nii.gz
```

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

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

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the DSI Studio workflow for autotrack registration.

```APIDOC
## init_dsi_studio_autotrack_registration_wf

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

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### QSIRecon DKI Reconstruction Derivatives

Source: https://qsirecon.readthedocs.io/en/latest/outputs.html

Example output structure for the DKI reconstruction method, detailing dataset description, HTML reports, logs, and DWI-specific parameter maps.

```plaintext
qsirecon/
   derivatives/
      qsirecon-DKI/
         dataset_description.json
         sub-<label>[_ses-<label>].html
         logs/
         sub-<label>/[ses-<label>/]
            figures/
            dwi/
               <source_entities>_model-dki_param-ad_dwimap.json
               <source_entities>_model-dki_param-ad_dwimap.nii.gz
               <source_entities>_model-dki_param-ak_dwimap.json
               <source_entities>_model-dki_param-ak_dwimap.nii.gz
               <source_entities>_model-dki_param-kfa_dwimap.json
               <source_entities>_model-dki_param-kfa_dwimap.nii.gz
               <source_entities>_model-dki_param-md_dwimap.json
               <source_entities>_model-dki_param-md_dwimap.nii.gz
               <source_entities>_model-dki_param-mk_dwimap.json
               <source_entities>_model-dki_param-mk_dwimap.nii.gz
               <source_entities>_model-dki_param-mkt_dwimap.json
               <source_entities>_model-dki_param-mkt_dwimap.nii.gz
               <source_entities>_model-dki_param-rd_dwimap.json
               <source_entities>_model-dki_param-rd_dwimap.nii.gz
               <source_entities>_model-dki_param-rk_dwimap.json
               <source_entities>_model-dki_param-rk_dwimap.nii.gz
               <source_entities>_model-tensor_param-fa_dwimap.json
               <source_entities>_model-tensor_param-fa_dwimap.nii.gz
               # Microstructural metrics calculated if wmti is True
               <source_entities>_model-dkimicro_param-awf_dwimap.json
               <source_entities>_model-dkimicro_param-awf_dwimap.nii.gz
               <source_entities>_model-dkimicro_param-rde_dwimap.json
               <source_entities>_model-dkimicro_param-rde_dwimap.nii.gz
```

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

### qsirecon.workflows.recon.dipy.init_dipy_dki_recon_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the Dipy reconstruction workflow for DKI.

```APIDOC
## init_dipy_dki_recon_wf

### Description
Initializes the Dipy reconstruction workflow for DKI.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### Get Spherical Harmonics L and M values

Source: https://qsirecon.readthedocs.io/en/latest/api/qsirecon.interfaces.anatomical.html

Generates the L (degree) and M (order) values for a given maximum spherical harmonics order (lmax). This is a helper function for SH-based analyses.

```python
from qsirecon.interfaces.anatomical import get_l_m

# Example: Get L and M values for lmax = 4
l_values, m_values = get_l_m(4)
```

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

### qsirecon.workflows.recon.amico.init_amico_noddi_fit_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the AMICO reconstruction workflow for NODDI fitting.

```APIDOC
## init_amico_noddi_fit_wf

### Description
Initializes the AMICO reconstruction workflow for NODDI fitting.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### Pipeline Node Example: CSD Reconstruction

Source: https://qsirecon.readthedocs.io/en/latest/_sources/building_workflows.rst.txt

Represents a processing unit for CSD (Constrained Spherical Deconvolution). It specifies the action, a unique name, parameters for the CSD algorithm, a suffix for the output, and the software to use (MRTrix3).

```yaml
nodes:
  -   action: csd
      name: msmt_csd
      parameters:
          fod:
              algorithm: msmt_csd
              max_sh:
              - 8
              - 8
              - 8
          mtnormalize: true
          response:
              algorithm: dhollander
      qsirecon_suffix: MRtrix3_act-FAST
      software: MRTrix3
```

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

### qsirecon.workflows.recon.utils.init_test_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes a test workflow.

```APIDOC
## init_test_wf

### Description
Initializes a test workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### Pipeline-level Metadata Example

Source: https://qsirecon.readthedocs.io/en/latest/_sources/building_workflows.rst.txt

Defines the name of the pipeline and lists additional computations based on anatomical images. The 'name' field determines the working directory, and 'anatomical' specifies computations like MRtrix_ 5tt segmentation.

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

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

### Building Local QSIRecon Docker Image

Source: https://qsirecon.readthedocs.io/en/latest/_sources/contributors.rst.txt

Build a local Docker image named 'qsirecon' from the working QSIRecon repository. This command should be run from the root of the repository.

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

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

### qsirecon.workflows.recon.mrtrix.init_mrtrix_csd_recon_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the MRTrix CSD reconstruction workflow.

```APIDOC
## init_mrtrix_csd_recon_wf

### Description
Initializes the MRTrix CSD reconstruction workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### qsirecon.workflows.recon.dipy.init_dipy_mapmri_recon_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the Dipy reconstruction workflow for MAPMRI.

```APIDOC
## init_dipy_mapmri_recon_wf

### Description
Initializes the Dipy reconstruction workflow for MAPMRI.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### Build Singularity/Apptainer Image for QSIRecon

Source: https://qsirecon.readthedocs.io/en/latest/installation.html

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

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

```

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

### Run QSIRecon with Apptainer

Source: https://qsirecon.readthedocs.io/en/latest/_sources/quickstart.rst.txt

This command demonstrates how to run the QSIRecon workflow using Apptainer. It specifies input and output directories, participant mode, working directory, number of threads, the reconstruction specification, and verbosity.

```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
```

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

### qsirecon.workflows.recon.utils.init_gradient_select_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes a workflow to select gradients.

```APIDOC
## init_gradient_select_wf

### Description
Initializes a workflow to select gradients.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### Run QSIRecon with Singularity/Apptainer

Source: https://qsirecon.readthedocs.io/en/latest/installation.html

Execute QSIRecon using a Singularity/Apptainer image. Bind necessary directories for data, output, and the Freesurfer license. Use --containall and --writable-tmpfs for isolation and temporary filesystem.

```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_pyafq_wf

Source: https://qsirecon.readthedocs.io/en/latest/api/qsirecon.workflows.recon.pyafq.html

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

```APIDOC
## init_pyafq_wf

### Description
Initializes and runs the PyAFQ workflow to generate tract profiles from qsirecon outputs. This function takes a dictionary of inputs, an optional workflow name, a qsirecon suffix, and a dictionary of parameters.

### Method
N/A (Python function)

### Endpoint
N/A (Python function)

### Parameters
#### Path Parameters
N/A

#### Query Parameters
N/A

#### Request Body
*   **_inputs_dict_** (dict) - Required - A dictionary containing qsirecon outputs.
*   **_name_** (str) - Optional - The name of the workflow. Defaults to 'afq'.
*   **_qsirecon_suffix_** (str) - Optional - A suffix for qsirecon outputs.
*   **_params_** (dict) - Optional - A dictionary of parameters for PyAFQ.

### Request Example
N/A (Python function)

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

#### Response Example
N/A (Python function)
```

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

### init_qsirecon_wf

Source: https://qsirecon.readthedocs.io/en/latest/api/qsirecon.workflows.base.html

Organizes the execution of qsirecon, with a sub-workflow for each subject.

```APIDOC
## init_qsirecon_wf

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

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

### Endpoint
Not applicable (Python function)

### Parameters
None specified
```

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

### Mounting Local Repositories with Docker

Source: https://qsirecon.readthedocs.io/en/latest/_sources/contributors.rst.txt

Mount local QSIRecon and Nipype repositories into the Docker container for testing changes without rebuilding the image. Use the '-v' flag for volume mounts.

```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
```

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

### Build Singularity/Apptainer Image

Source: https://qsirecon.readthedocs.io/en/latest/_sources/installation.rst.txt

Build a Singularity/Apptainer image for QSIRecon from the Docker repository. Replace <version> with the specific QSIRecon version you need.

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

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

### qsirecon.interfaces.converters.popen_run

Source: https://qsirecon.readthedocs.io/en/latest/api/qsirecon.interfaces.converters.html

Builds and runs applications using a list of arguments.

```APIDOC
## popen_run

### Description
Build and run apps in over 115 regions with MongoDB Atlas, the database for every enterprise.

### Parameters
#### Path Parameters
- **arg_list** (list) - Required - List of arguments for the application.
```

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

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

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the main DWI reconstruction workflow.

```APIDOC
## init_dwi_recon_workflow

### Description
Initializes the main DWI reconstruction workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### qsirecon.workflows.recon.utils.init_scalar_output_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes a workflow for scalar output.

```APIDOC
## init_scalar_output_wf

### Description
Initializes a workflow for scalar output.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### qsirecon.workflows.reports.init_json_preproc_report_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

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 function call)

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

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

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes a workflow to convert QSIrecon outputs to FSL format.

```APIDOC
## init_qsirecon_to_fsl_wf

### Description
Initializes a workflow to convert QSIrecon outputs to FSL format.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### qsirecon.workflows.recon.dipy.init_dipy_mapmri_recon_wf

Source: https://qsirecon.readthedocs.io/en/latest/api/qsirecon.workflows.recon.dipy.html

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

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

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

### Inputs
- _qsirecon outputs_

### Outputs
- **shore_coeffs** (_str_): 3dSHORE coefficients.
- **rtop** (_str_): Voxelwise Return-to-origin probability.
- **rtap** (_str_): Voxelwise Return-to-axis probability.
- **rtpp** (_str_): Voxelwise Return-to-plane probability.
- **msd** (_str_): Voxelwise MSD.
- **qiv** (_str_): q-space inverse variance.
- **lapnorm** (_str_): Voxelwise norm of the Laplacian.

### Parameters
- **_name** (_str_): Name of the workflow. Defaults to 'dipy_mapmri_recon'.
- **_qsirecon_suffix** (_str_): Suffix for the qsirecon outputs.
- **_params** (_dict_): Dictionary containing the parameters for the workflow.
  - **write_fibgz** (bool): True writes out a DSI Studio fib file.
  - **write_mif** (bool): True writes out a MRTrix mif file with sh coefficients.
  - **radial_order** (int): An even integer that represents the order of the basis.
  - **laplacian_regularization** (bool): Regularize using the Laplacian of the MAP-MRI basis.
  - **laplacian_weighting** (str or scalar): The string ‘GCV’ makes it use generalized cross-validation to find the regularization weight. A scalar sets the regularization weight to that value and an array will make it selected the optimal weight from the values in the array.
  - **positivity_constraint** (bool): Use positivity constraint.
```

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

### qsirecon.workflows.recon.converters.init_mif_to_fibgz_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes a workflow to convert MIF files to FIB/GZ format.

```APIDOC
## init_mif_to_fibgz_wf

### Description
Initializes a workflow to convert MIF files to FIB/GZ format.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### qsirecon.workflows.base.init_single_subject_recon_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the reconstruction workflow for a single subject.

```APIDOC
## init_single_subject_recon_wf

### Description
Initializes the reconstruction workflow for a single subject.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### qsirecon.workflows.recon.converters.init_fibgz_to_mif_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes a workflow to convert FIB/GZ files to MIF format.

```APIDOC
## init_fibgz_to_mif_wf

### Description
Initializes a workflow to convert FIB/GZ files to MIF format.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

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

Source: https://qsirecon.readthedocs.io/en/latest/api/qsirecon.workflows.recon.dipy.html

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

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

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

### Inputs
- _qsirecon outputs_

### Outputs
- **shore_coeffs** (_str_): 3dSHORE coefficients
- **rtop** (_str_): Voxelwise Return-to-origin probability.
- **rtap** (_str_): Voxelwise Return-to-axis probability.
- **rtpp** (_str_): Voxelwise Return-to-plane probability.

### Parameters
- **_name** (_str_): Name of the workflow. Defaults to 'dipy_3dshore_recon'.
- **_qsirecon_suffix** (_str_): Suffix for the qsirecon outputs.
- **_params** (_dict_): Dictionary containing the parameters for the workflow.
  - **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”, “lifespan” will resample the data with this scheme.
  - **radial_order** (int): Radial order for spherical harmonics (even).
  - **zeta** (float): Zeta parameter for basis set.
  - **tau** (float): Diffusion parameter (default= 4 * np.pi**2).
  - **regularization** (str): “L2” or “L1”. Default is “L2”.
  - **lambdaN** (float): LambdaN parameter for L2 regularization. (default=1e-8).
  - **lambdaL** (float): LambdaL parameter for L2 regularization. (default=1e-8).
  - **regularization_weighting** (int or "CV"): L1 regualrization weighting. Default “CV” (use cross-validation). Can specify a static value to use in all voxels.
  - **l1_positive_constraint** (bool): Use positivity constraint.
  - **l1_maxiter** (int): Maximum number of iterations for L1 optization. (Default=1000).
  - **l1_alpha** (float): Alpha parameter for L1 optimization. (default=1.0).
  - **pos_grid** (int): Grid points for estimating EAP(default=11).
  - **pos_radius** (float): Radius for EAP estimation (default=20e-03).
```

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

### init_qsirecon_to_fsl_wf

Source: https://qsirecon.readthedocs.io/en/latest/api/qsirecon.workflows.recon.converters.html

Converts QSIRecon outputs to FSL standard orientation, including images, bval, and bvec files.

```APIDOC
## init_qsirecon_to_fsl_wf

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

### Inputs
* `_inputs_dict_` (dict) - Dictionary containing QSIRecon output files.

### Outputs
* (Implicitly, FSL standard files)

### Parameters
* `_name` (string) - Optional - Name of the workflow, defaults to 'qsirecon_to_fsl'.
* `_qsirecon_suffix` (string) - Optional - Suffix for QSIRecon outputs.
* `_params` (dict) - Optional - Parameters for the workflow.
```

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

### qsirecon.workflows.recon.pyafq.init_pyafq_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the PyAFQ workflow for tractometry and visualization.

```APIDOC
## init_pyafq_wf

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

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

### Mounting Local Repositories with Singularity

Source: https://qsirecon.readthedocs.io/en/latest/_sources/contributors.rst.txt

Bind mount local QSIRecon source code into a Singularity container for development. This allows testing changes without rebuilding the image.

```bash
$ singularity run \
    -B $HOME/projects/qsirecon/qsirecon:/usr/local/miniconda/lib/python3.10/site-packages/qsirecon \
    qsirecon.img \
    /scratch/dataset /scratch/out participant -w /out/work/
```

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

### Run QSIRecon with Singularity/Apptainer

Source: https://qsirecon.readthedocs.io/en/latest/_sources/installation.rst.txt

Execute QSIRecon using a Singularity/Apptainer image. This command binds necessary directories and the FreeSurfer license file. Replace <version> with the image version.

```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
```

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

### qsirecon.workflows.recon.mrtrix.init_mrtrix_tractography_wf

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes the MRTrix tractography workflow.

```APIDOC
## init_mrtrix_tractography_wf

### Description
Initializes the MRTrix tractography workflow.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```

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

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

Source: https://qsirecon.readthedocs.io/en/latest/api_reference.html

Initializes a workflow to register FreeSurfer outputs to QSIPrep space.

```APIDOC
## init_register_fs_to_qsiprep_wf

### Description
Initializes a workflow to register FreeSurfer outputs to QSIPrep space.

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

### Endpoint
Not specified

### Parameters
Not specified

### Request Example
Not specified

### Response
Not specified
```
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