Metadata-Version: 2.1
Name: surfdist
Version: 0.15.5
Summary: For calculating exact geodesic distances on cortical surface meshes
Home-page: https://github.com/NeuroanatomyAndConnectivity/surfdist
Author: Daniel Margulies
Author-email: daniel.margulies@gmail.com
License: LICENSE.txt
Description: surfdist
        ========
        [![Build Status](https://travis-ci.com/NeuroanatomyAndConnectivity/surfdist.svg?branch=master)](https://travis-ci.com/NeuroanatomyAndConnectivity/surfdist)
        
        Calculate the exact geodesic distance on a triangular surface mesh using the [gdist package](https://pypi.python.org/pypi/gdist/), which is based on the [c++ library](https://code.google.com/p/geodesic/).
        
        Installation
        ------------
        
            pip install surfdist
        
        Example
        -------
        
            import nibabel as nib
            import numpy as np
            import matplotlib.pyplot as plt
            import os
            import surfdist as sd
            from surfdist import viz, load, utils, analysis
        
            # calculate and display distance from central sulcus at each node:
            cmap = 'coolwarm'
            base_dir = '/Applications/freesurfer/subjects/'
            surf = nib.freesurfer.read_geometry(os.path.join(base_dir, 'bert/surf/lh.pial'))
            cort = np.sort(nib.freesurfer.read_label(os.path.join(base_dir, 'bert/label/lh.cortex.label')))
            sulc = nib.freesurfer.read_morph_data(os.path.join(base_dir, 'bert/surf/lh.sulc'))
        
            # load central sulcus nodes
            src  = sd.load.load_freesurfer_label(os.path.join(base_dir, 'bert/label/lh.aparc.a2009s.annot'), 'S_central', cort)
        
            # calculate distance
            dist = sd.analysis.dist_calc(surf, cort, src)
        
            # visualize
            plot_med = sd.viz.viz(surf[0], surf[1], dist, bg_map=sulc, bg_on_stat=True, cmap=cmap)
            plot_lat = sd.viz.viz(surf[0], surf[1], dist, azim=180, bg_map=sulc, bg_on_stat=True, cmap=cmap)
        
            # Calculate distances on native surface and display on fsaverage
            fsa4 = nib.freesurfer.read_geometry(os.path.join(base_dir,'fsaverage4/surf/lh.sphere.reg'))[0]
            fsa4_sulc=nib.freesurfer.read_morph_data(os.path.join(base_dir, 'fsaverage4/surf/lh.sulc'))
            native = nib.freesurfer.read_geometry(os.path.join(base_dir, 'bert/surf/lh.sphere.reg'))[0]
            idx_fsa4_to_native = sd.utils.find_node_match(fsa4, native)[0]
        
            surf_fsa4 = nib.freesurfer.read_geometry(os.path.join(base_dir, 'fsaverage4/surf/lh.pial'))
            plot_fsa4_med = sd.viz.viz(surf_fsa4[0], surf_fsa4[1], dist[idx_fsa4_to_native], bg_map=fsa4_sulc, bg_on_stat=True, cmap=cmap)
            plot_fsa4_lat = sd.viz.viz(surf_fsa4[0], surf_fsa4[1], dist[idx_fsa4_to_native], azim=180, bg_map=fsa4_sulc, bg_on_stat=True, cmap=cmap)
        
            plt.show()
        
Keywords: geodesic,distance,brain,cortex
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
