diff --git a/docs/usage.rst b/docs/usage.rst
index 358453e7..a02fbe9f 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -11,7 +11,7 @@ To utilize Eddymotion functionalities within your Python module or script, follo
.. code-block:: python
# Import required components from the Eddymotion package
- from eddymotion.data.dmri import DWI
+ from eddymotion.data import dmri
from eddymotion.estimator import EddyMotionEstimator
2. **Load DWI Data**: Load diffusion MRI (dMRI) data into a `DWI` object using the `load` function. Ensure the gradient table is provided. It should have one row per diffusion-weighted image. The first three columns represent the gradient directions, and the last column indicates the timing and strength of the gradients in units of s/mm² [ R A S+ b ]. If your data are in NIfTI file format, include a file containing the gradient information with the argument "gradients_file":
@@ -19,9 +19,17 @@ To utilize Eddymotion functionalities within your Python module or script, follo
.. code-block:: python
# Load dMRI data into a DWI object
- dwi_data = DWI.load('/path/to/your/dwi_data.nii.gz', gradients_file='/path/to/your/gradient_file')
+ dwi_data = dmri.load('/path/to/your/dwi_data.nii.gz', gradients_file='/path/to/your/gradient_file')
- *Note*: To run the examples and tests from this page, you can download an example of DWI data from `here `_.
+ .. note::
+
+ To run the examples and tests from this page,
+ find `sample data `__ on OSF.
+ To load from an HDF5 file, use:
+
+ .. code-block:: python
+
+ dwi_data = dmri.DWI.from_filename('/path/to/downloaded/dwi_full.h5')
3. **Instantiate an Eddymotion Estimator Object**: Create an instance of the `EddyMotionEstimator` class, which encapsulates tools for estimating rigid-body head motion and distortions due to eddy currents.
@@ -56,7 +64,8 @@ To utilize Eddymotion functionalities within your Python module or script, follo
- `n_jobs`: Number of parallel jobs.
- `seed`: Seed for the random number generator (necessary for deterministic estimation).
- The method returns a list of affine matrices encoding the estimated parameters of the deformations due to head motion and eddy currents.
+ The method returns an Nx4x4 array of affine matrices encoding the estimated parameters of
+ the deformations due to head motion and eddy currents.
Example:
@@ -100,5 +109,3 @@ To utilize Eddymotion functionalities within your Python module or script, follo
dwi_data.plot_mosaic(index=0)
# Visualize gradients
dwi_data.plot_gradients()
-
-