Mercurial > repos > greg > create_streamlines

comparison create_streamlines.py @ 6:606a712b6322 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Wed, 29 Nov 2017 09:50:51 -0500
parents 3b5e09c727f5
children 1f1fdfe9ac4d
comparison
equal deleted inserted replaced
5:c55029873167 6:606a712b6322
77 dm = utils.density_map(lr_superiorfrontal_track, shape, affine=affine) 77 dm = utils.density_map(lr_superiorfrontal_track, shape, affine=affine)
78 # Save density map 78 # Save density map
79 dm_img = nib.Nifti1Image(dm.astype("int16"), hardi_img.affine) 79 dm_img = nib.Nifti1Image(dm.astype("int16"), hardi_img.affine)
80 dm_img.to_filename("lr-superiorfrontal-dm.nii") 80 dm_img.to_filename("lr-superiorfrontal-dm.nii")
81 shutil.move('lr-superiorfrontal-dm.nii', args.output_superiorfrontal_nifti) 81 shutil.move('lr-superiorfrontal-dm.nii', args.output_superiorfrontal_nifti)
82
83 # Make a trackvis header so we can save streamlines 82 # Make a trackvis header so we can save streamlines
84 voxel_size = labels_img.header.get_zooms() 83 voxel_size = labels_img.header.get_zooms()
85 trackvis_header = nib.trackvis.empty_header() 84 trackvis_header = nib.trackvis.empty_header()
86 trackvis_header['voxel_size'] = voxel_size 85 trackvis_header['voxel_size'] = voxel_size
87 trackvis_header['dim'] = shape 86 trackvis_header['dim'] = shape
88 trackvis_header['voxel_order'] = "RAS" 87 trackvis_header['voxel_order'] = "RAS"
89
90 # Move streamlines to "trackvis space" 88 # Move streamlines to "trackvis space"
91 trackvis_point_space = utils.affine_for_trackvis(voxel_size) 89 trackvis_point_space = utils.affine_for_trackvis(voxel_size)
92 lr_sf_trk = utils.move_streamlines(lr_superiorfrontal_track, trackvis_point_space, input_space=affine) 90 lr_sf_trk = utils.move_streamlines(lr_superiorfrontal_track, trackvis_point_space, input_space=affine)
93 lr_sf_trk = list(lr_sf_trk) 91 lr_sf_trk = list(lr_sf_trk)
94
95 # Save streamlines 92 # Save streamlines
96 for_save = [(sl, None, None) for sl in lr_sf_trk] 93 for_save = [(sl, None, None) for sl in lr_sf_trk]
97 nib.trackvis.write("lr-superiorfrontal.trk", for_save, trackvis_header) 94 nib.trackvis.write("lr-superiorfrontal.trk", for_save, trackvis_header)
98 shutil.move('lr-superiorfrontal.trk', args.output_trackvis_header) 95 shutil.move('lr-superiorfrontal.trk', args.output_trackvis_header)
99 dm_trackvis = utils.density_map(lr_sf_trk, shape, affine=trackvis_point_space)
100 assert np.all(dm == dm_trackvis)