Mercurial > repos > greg > create_streamlines
comparison create_streamlines.py @ 6:606a712b6322 draft
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) |