Update documentation for noddi/freewater addition

src/content/docs/guides/outputs.mdx

@@ -192,6 +192,28 @@ The `dwi/` folder contains diffusion preprocessing outputs, local modeling resul
 - `*_space-DWI_label-exclude_desc-pft_probseg.nii.gz`: Exclude probability map for PFT tracking.
 - `*_space-DWI_label-include_desc-pft_probseg.nii.gz`: Include probability map for PFT tracking.
 
+#### Freewater Elimination (and freewater-corrected maps)
+
+- `*_desc-fwc_dwi.nii.gz`: Freewater-corrected DWI image.
+- `*_model-tensor_param-fa_desc-fwc_dwimap.nii.gz`: Freewater-corrected fractional anisotropy (FA) map in native diffusion space.
+- `*_model-tensor_param-md_desc-fwc_dwimap.nii.gz`: Freewater-corrected mean diffusivity (MD) map in native diffusion space.
+- `*_model-tensor_param-ad_desc-fwc_dwimap.nii.gz`: Freewater-corrected axial diffusivity (AD) map in native diffusion space.
+- `*_model-tensor_param-rd_desc-fwc_dwimap.nii.gz`: Freewater-corrected radial diffusivity (RD) map in native diffusion space.
+- `*_model-tensor_param-mode_desc-fwc_dwimap.nii.gz`: Freewater-corrected mode map in native diffusion space.
+- `*_model-tensor_param-ga_desc-fwc_dwimap.nii.gz`: Freewater-corrected geodesic anisotropy (GA) map in native diffusion space.
+- `*_model-tensor_param-rgb_desc-fwc_dwimap.nii.gz`: Freewater-corrected color-coded directional FA map in native diffusion space.
+- `*_model-tensor_param-diffusivity_desc-fwc_dwimap.nii.gz`: Freewater-corrected tensor diffusivity in native diffusion space.
+- `*_space-{template}_model-tensor_param-{fa,md,ad,rd,mode,ga,rgb}_desc-fwc_dwimap.nii.gz`: Freewater-corrected DTI metrics in template space.
+
+#### NODDI
+
+- `*_model-noddi_param-direction_dwimap.nii.gz`: Primary neurite orientation direction map in native diffusion space.
+- `*_model-noddi_param-fwf_dwimap.nii.gz`: Free water fraction (FWF) map in native diffusion space.
+- `*_model-noddi_param-icvf_dwimap.nii.gz`: Intracellular volume fraction (ICVF) map in native diffusion space.
+- `*_model-noddi_param-isovf_dwimap.nii.gz`: Isotropic volume fraction (ISOVF) map in native diffusion space.
+- `*_model-noddi_param-odi_dwimap.nii.gz`: Orientation dispersion index (ODI) map in native diffusion space.
+- `*_space-{template}_model-noddi_param-{fwf,icvf,isovf,odi}_dwimap.nii.gz`: NODDI metrics in template space.
+
 #### Bundles (in `bundles/` subdirectory)
 
 - `*_tract-{bundleName}_hemi-{left,right}_track-sdstream_tractogram.trk`: Individual bundle tractograms (cleaned, uniformized, and colored).

src/content/docs/guides/parameters.md

@@ -220,6 +220,39 @@ Options for local tracking.
 | `local_min_len` | Minimum length used in the local tracking step. | `number` | 20 |  | False |
 | `local_max_len` | Maximum length used in the local tracking step. | `number` | 200 |  | False |
 
+### **Diffusivities Options**
+
+Parameters for tuning diffusivities used in models fitting
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `average_diff_priors` | If set to true, will compute the average diffusivities for the NODDI/Freewater models and average them across all subjects to use as fixed diffusivities for all subjects. | `boolean` | False |  | False |
+| `para_diff` | Parallel diffusivity value to use in models fitting (in mm^2/s). If not set, it will be derived from normative growth curves based on participant's age. | `number` |  |  | False |
+| `iso_diff` | Isotropic diffusivity value to use in models fitting (in mm^2/s). If not set, it will be derived from normative growth curves based on participant's age. | `number` |  |  | False |
+| `perp_diff` | Perpendicular diffusivity value to use in models fitting (in mm^2/s). If not set, it will be derived from normative growth curves based on participant's age. | `number` |  |  | False |
+| `perp_diff_min` | Minimum perpendicular diffusivity value (in mm^2/s) to use in models fitting. If not set, it will be derived from normative growth curves based on participant's age | `number` |  |  | False |
+| `perp_diff_max` | Maximum perpendicular diffusivity value (in mm^2/s) to use in models fitting. If not set, it will be derived from normative growth curves based on participant's age | `number` |  |  | False |
+
+### **NODDI Options**
+
+Options for NODDI model fitting.
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `run_noddi` | Whether to run the NODDI processing step. If selected, the resulting metric maps will be added to the list used in the bundling and connectomics profile. | `boolean` | False |  | False |
+| `noddi_lambda1` | Value to use as the first regularization parameter (lambda1) in the NODDI fitting process. | `number` | 0.5 |  | True |
+| `noddi_lambda2` | Value to use as the second regularization parameter (lambda2) in the NODDI fitting process. | `number` | 0.001 |  | True |
+
+### **Freewater Options**
+
+Options for Freewater model fitting.
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `run_freewater` | Whether to run the Freewater processing step. If selected, the resulting metric maps will be added to the list used in the bundling and connectomics profile. | `boolean` | False |  | False |
+| `freewater_lambda1` | Value to use as the first regularization parameter (lambda1) in the Freewater fitting process. | `number` | 0 |  | True |
+| `freewater_lambda2` | Value to use as the second regularization parameter (lambda2) in the Freewater fitting process. | `number` | 0.25 |  | True |
+
 ### **BundleSeg Options**
 
 Options for BundleSeg
@@ -262,9 +295,6 @@ Options for COMMIT filtering.
 |-----------|-----------|-----------|-----------|-----------|-----------|
 | `run_commit2` | Run COMMIT2 filtering. | `boolean` | True |  | False |
 | `commit2_lambda` | Lambda value used in the COMMIT filtering step. | `number` | 0.001 |  | True |
-| `commit_para_diff` | Para diff value used in the COMMIT filtering step. <details><summary>Help</summary><small>This value is derived from normative curves in function of each participant's age. For more information, please see [the documentation](https://scilus.github.io/sf-pediatric/guides/priors/).</small></details>| `string` |  |  | False |
-| `commit_iso_diff` | Iso diff value used in the COMMIT filtering step. <details><summary>Help</summary><small>This value is derived from normative curves in function of each participant's age. For more information, please see [the documentation](https://scilus.github.io/sf-pediatric/guides/priors/).</small></details>| `string` |  |  | False |
-| `commit_perp_diff` | Perp diff value used in the COMMIT filtering step. <details><summary>Help</summary><small>This value is derived from normative curves in function of each participant's age. For more information, please see [the documentation](https://scilus.github.io/sf-pediatric/guides/priors/).</small></details>| `string` |  |  | False |
 | `commit_ball_stick` | Use the ball and stick model in the COMMIT filtering step. | `boolean` | False |  | True |
 | `commit_nbr_dir` | Number of directions used in the COMMIT filtering step. | `integer` | 500 |  | True |
 

src/content/docs/guides/priors.mdx

@@ -10,7 +10,7 @@ One innovative feature of `sf-pediatric` is how it uses normative curves of diff
 ![curves](../../../assets/normative_curves_and_rawdata.png)
 
 :::note
-While only the FRF and COMMIT priors are currently supported using normative curves, we are working to extend this method to other processing aspects to ensure the most optimal age appropriate processing of diffusion MRI acquisitions.
+While only the FRF, COMMIT, Freewater Elimination, and NODDI priors are currently supported using normative curves, we are working to extend this method to other processing aspects to ensure the most optimal age appropriate processing of diffusion MRI acquisitions. If you would like to see a new use case implemented, feel free to [open an issue on GitHub](https://github.com/scilus/sf-pediatric.git).
 :::
 
-Each of those median normative curves were approximate using single equations, and implemented into `sf-pediatric`. While this is the default option, users can still specify their own FRF using the parameter [`--frf_manual_frf`](/sf-pediatric/guides/parameters/#frf-options). Similarly, COMMIT priors can be specified with [`--commit_para_diff`](/sf-pediatric/guides/parameters/#commit-options), [`--commit_perp_diff`](/sf-pediatric/guides/parameters/#commit-options), and [`--commit_iso_diff`](/sf-pediatric/guides/parameters/#commit-options).
+Each of those median normative curves were approximate using single equations, and implemented into `sf-pediatric`. While this is the default option, users can still specify their own FRF using the parameter [`--frf_manual_frf`](/sf-pediatric/guides/parameters/#frf-options). Similarly, Freewater Elimination, NODDI, and COMMIT priors can be specified with [`--para_diff`](/sf-pediatric/guides/parameters/#diffusivities-options), [`--perp_diff`](/sf-pediatric/guides/parameters/#diffusivities-options), [`--iso_diff`](/sf-pediatric/guides/parameters/#diffusivities-options), [`--perp_diff_min`](/sf-pediatric/guides/parameters/#diffusivities-options), and [`--perp_diff_max`](/sf-pediatric/guides/parameters/#diffusivities-options).