""" ========================= Calculate Path Length Map ========================= We show how to calculate a Path Length Map for Anisotropic Radiation Therapy Contours given a set of streamlines and a region of interest (ROI). The Path Length Map is a volume in which each voxel's value is the shortest distance along a streamline to a given region of interest (ROI). This map can be used to anisotropically modify radiation therapy treatment contours based on a tractography model of the local white matter anatomy, as described in [Jordan_2018_plm]_, by executing this tutorial with the gross tumor volume (GTV) as the ROI. NOTE: The background value is set to -1 by default """ from dipy.core.gradients import gradient_table from dipy.data import get_fnames, default_sphere from dipy.io.gradients import read_bvals_bvecs from dipy.io.image import load_nifti_data, load_nifti, save_nifti from dipy.reconst.shm import CsaOdfModel from dipy.direction import peaks_from_model from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion from dipy.tracking import utils from dipy.tracking.local_tracking import LocalTracking from dipy.tracking.streamline import Streamlines from dipy.viz import actor, window, colormap as cmap from dipy.tracking.utils import path_length import numpy as np import matplotlib as mpl from mpl_toolkits.axes_grid1 import AxesGrid """ First, we need to generate some streamlines and visualize. For a more complete description of these steps, please refer to the :ref:`example_probabilistic_fiber_tracking` and the Visualization of ROI Surface Rendered with Streamlines Tutorials. """ hardi_fname, hardi_bval_fname, hardi_bvec_fname = get_fnames('stanford_hardi') label_fname = get_fnames('stanford_labels') data, affine, hardi_img = load_nifti(hardi_fname, return_img=True) labels = load_nifti_data(label_fname) bvals, bvecs = read_bvals_bvecs(hardi_bval_fname, hardi_bvec_fname) gtab = gradient_table(bvals, bvecs) white_matter = (labels == 1) | (labels == 2) csa_model = CsaOdfModel(gtab, sh_order=6) csa_peaks = peaks_from_model(csa_model, data, default_sphere, relative_peak_threshold=.8, min_separation_angle=45, mask=white_matter) stopping_criterion = ThresholdStoppingCriterion(csa_peaks.gfa, .25) """ We will use an anatomically-based corpus callosum ROI as our seed mask to demonstrate the method. In practice, this corpus callosum mask (labels == 2) should be replaced with the desired ROI mask (e.g. gross tumor volume (GTV), lesion mask, or electrode mask). """ # Make a corpus callosum seed mask for tracking seed_mask = labels == 2 seeds = utils.seeds_from_mask(seed_mask, affine, density=[1, 1, 1]) # Make a streamline bundle model of the corpus callosum ROI connectivity streamlines = LocalTracking(csa_peaks, stopping_criterion, seeds, affine, step_size=2) streamlines = Streamlines(streamlines) # Visualize the streamlines and the Path Length Map base ROI # (in this case also the seed ROI) streamlines_actor = actor.line(streamlines, cmap.line_colors(streamlines)) surface_opacity = 0.5 surface_color = [0, 1, 1] seedroi_actor = actor.contour_from_roi(seed_mask, affine, surface_color, surface_opacity) scene = window.Scene() scene.add(streamlines_actor) scene.add(seedroi_actor) """ If you set interactive to True (below), the scene will pop up in an interactive window. """ interactive = False if interactive: window.show(scene) window.record(scene, n_frames=1, out_path='plm_roi_sls.png', size=(800, 800)) """ .. figure:: plm_roi_sls.png :align: center **A top view of corpus callosum streamlines with the blue transparent ROI in the center**. """ """ Now we calculate the Path Length Map using the corpus callosum streamline bundle and corpus callosum ROI. NOTE: the mask used to seed the tracking does not have to be the Path Length Map base ROI, as we do here, but it often makes sense for them to be the same ROI if we want a map of the whole brain's distance back to our ROI. (e.g. we could test a hypothesis about the motor system by making a streamline bundle model of the cortico-spinal track (CST) and input a lesion mask as our Path Length Map base ROI to restrict the analysis to the CST) """ path_length_map_base_roi = seed_mask # calculate the WMPL wmpl = path_length(streamlines, affine, path_length_map_base_roi) # save the WMPL as a nifti save_nifti('example_cc_path_length_map.nii.gz', wmpl.astype(np.float32), affine) # get the T1 to show anatomical context of the WMPL t1_fname = get_fnames('stanford_t1') t1_data = load_nifti_data(t1_fname) fig = mpl.pyplot.figure() fig.subplots_adjust(left=0.05, right=0.95) ax = AxesGrid(fig, 111, nrows_ncols=(1, 3), cbar_location="right", cbar_mode="single", cbar_size="10%", cbar_pad="5%") """ We will mask our WMPL to ignore values less than zero because negative numbers indicate no path back to the ROI was found in the provided streamlines """ wmpl_show = np.ma.masked_where(wmpl < 0, wmpl) slx, sly, slz = [60, 50, 35] ax[0].matshow(np.rot90(t1_data[:, slx, :]), cmap=mpl.cm.bone) im = ax[0].matshow(np.rot90(wmpl_show[:, slx, :]), cmap=mpl.cm.cool, vmin=0, vmax=80) ax[1].matshow(np.rot90(t1_data[:, sly, :]), cmap=mpl.cm.bone) im = ax[1].matshow(np.rot90(wmpl_show[:, sly, :]), cmap=mpl.cm.cool, vmin=0, vmax=80) ax[2].matshow(np.rot90(t1_data[:, slz, :]), cmap=mpl.cm.bone) im = ax[2].matshow(np.rot90(wmpl_show[:, slz, :]), cmap=mpl.cm.cool, vmin=0, vmax=80) ax.cbar_axes[0].colorbar(im) for lax in ax: lax.set_xticks([]) lax.set_yticks([]) fig.savefig("Path_Length_Map.png") """ .. figure:: Path_Length_Map.png :align: center **Path Length Map showing the shortest distance, along a streamline, from the corpus callosum ROI with the background set to -1**. References ---------- .. [Jordan_2018_plm] Jordan K. et al., "An Open-Source Tool for Anisotropic Radiation Therapy Planning in Neuro-oncology Using DW-MRI Tractography", PREPRINT (biorxiv), 2018. .. include:: ../links_names.inc """