Mercurial > repos > greg > create_streamlines
changeset 6:606a712b6322 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 29 Nov 2017 09:50:51 -0500 |
| parents | c55029873167 |
| children | 2d06191d7820 |
| files | create_streamlines.py |
| diffstat | 1 files changed, 0 insertions(+), 5 deletions(-) [+] |
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--- a/create_streamlines.py Wed Nov 29 09:50:42 2017 -0500 +++ b/create_streamlines.py Wed Nov 29 09:50:51 2017 -0500 @@ -79,22 +79,17 @@ dm_img = nib.Nifti1Image(dm.astype("int16"), hardi_img.affine) dm_img.to_filename("lr-superiorfrontal-dm.nii") shutil.move('lr-superiorfrontal-dm.nii', args.output_superiorfrontal_nifti) - # Make a trackvis header so we can save streamlines voxel_size = labels_img.header.get_zooms() trackvis_header = nib.trackvis.empty_header() trackvis_header['voxel_size'] = voxel_size trackvis_header['dim'] = shape trackvis_header['voxel_order'] = "RAS" - # Move streamlines to "trackvis space" trackvis_point_space = utils.affine_for_trackvis(voxel_size) lr_sf_trk = utils.move_streamlines(lr_superiorfrontal_track, trackvis_point_space, input_space=affine) lr_sf_trk = list(lr_sf_trk) - # Save streamlines for_save = [(sl, None, None) for sl in lr_sf_trk] nib.trackvis.write("lr-superiorfrontal.trk", for_save, trackvis_header) shutil.move('lr-superiorfrontal.trk', args.output_trackvis_header) -dm_trackvis = utils.density_map(lr_sf_trk, shape, affine=trackvis_point_space) -assert np.all(dm == dm_trackvis)