Created
December 9, 2011 14:51
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apply transforms to trackvis tracks.
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| from enthought.mayavi import mlab | |
| import streamlines | |
| import numpy as np | |
| from nibabel import load | |
| from colorsys import rgb_to_hsv | |
| # filename = "DeterministicTractography/QBALLRecon/hardiO10.trk" | |
| trkfilename = "/software/data/STUT/DTI_TV/PWS04/dtk_35/dti_35.trk" #%hardiO10.trk_cross_streamline_id_20.trk" | |
| bfilename = "/software/data/STUT/DTI_TV/PWS04/dt_recon/lowb.nii" | |
| mrfilename = "/software/data/MIBR/data/PWS04/head.nii" | |
| reg = np.genfromtxt('/software/data/STUT/DTI_TV/PWS04/dt_recon/register.dat',skiprows=4,comments='r') | |
| bimg = load(bfilename) | |
| mrimg = load(mrfilename) | |
| M = np.array([[-1,0,0,128], | |
| [0, 0, 1, -128], | |
| [0, -1, 0, 128], | |
| [0,0,0,1]],dtype=float) | |
| M1 = np.array([[-2,0,0,128], | |
| [0, 0, 2, -64], | |
| [0, -2, 0, 128], | |
| [0,0,0,1]],dtype=float) | |
| s = streamlines.Streamlines() | |
| s.loadTrk(trkfilename) | |
| s.printHeaderTrk() | |
| aff = bimg.get_affine() | |
| #xfm = np.dot(np.dot(np.dot(img2.get_affine(),np.linalg.inv(M)),reg),aff) | |
| xfm = np.dot(mrimg.get_affine(),np.dot(np.linalg.inv(M),np.dot(np.linalg.inv(reg),M1))) | |
| print xfm | |
| #s.affineTransform(np.dot(aff[0:3,0:3],np.diag(1./s.header['voxel_size'])),aff[0:3,3]) | |
| s.affineTransform(np.dot(xfm[0:3,0:3],np.diag(1./s.header['voxel_size'])),xfm[0:3,3]) |
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