From 3f5f837c8dcdc2afba28496a8b45637c20b06019 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 16 May 2024 07:48:50 -0400 Subject: [PATCH] DOC: Fix data load instructions, correct estimated_affines type description --- docs/usage.rst | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) 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() - -