for s_id in np.arange(len(source_ids)): print '-----------------------------------------------------------------------------------------' print 'Source: ', source_ids[s_id] source = str(source_ids[s_id]) flirt_filename = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Code/data/' + source+'/DIFF2DEPI_EKJ_64dirs_14/DTI/flirt.mat' fa_filename= '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + source + '/DTI/dti_fa_brain.nii.gz' tracks_filename = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + source + '/DTI/dti.trk' linear_filename = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + source + '/DTI/dti_linear.dpy' warp_tracks_linearly(flirt_filename,fa_filename, tracks_filename,linear_filename) print 'Saved ', linear_filename tract_linear = load_whole_tract(linear_filename) if save: from common_functions import save_tract_trk fa_warped = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Code/data/' + source+'/DIFF2DEPI_EKJ_64dirs_14/DTI/fa_warped.nii.gz' fname_out = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + source + '/DTI/dti_linear.trk' save_tract_trk(tract_linear, fa_warped, fname_out ) print 'Saved ', fname_out if vis: tract = load_whole_tract(tracks_filename) from dipy.viz import fvtk from common_functions import visualize_tract ren = fvtk.ren() visualize_tract(ren, tract,color=fvtk.red) visualize_tract(ren, tract_linear,color=fvtk.blue) fvtk.show(ren) clearall()
cst_ext_vtk_fname = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + subj + '_cst_L_tvis_ext.vtk' ''' #CST_Right #saving CST as trk file s_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/tvis_tractography/' + subj + '_tracks_dti_tvis.trk' #cst_ind = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + subj + '_corticospinal_R_tvis.pkl' #cst_tract = load_tract(s_file,cst_ind) cst_ext_ind = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/50_SFF_in_ext/ROI_seg_native/' + subj + '_cst_R_tvis_ext.pkl' cst_tract_ext = load_tract(s_file,cst_ext_ind) s_fa = '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + subj + '/DTI/dti_fa_brain.nii.gz' #cst_trk_fname = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + subj + '_corticospinal_R_tvis.trk' #save_tract_trk(cst_tract, s_fa, cst_trk_fname) cst_ext_trk_fname = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + subj + '_cst_R_tvis_ext.trk' save_tract_trk(cst_tract_ext, s_fa, cst_ext_trk_fname) #converting trk file to vtk file input_anatomy_ref = '/home/bao/tiensy/Lauren_registration/data_compare_mapping/anatomy/' + subj + '_data_brain.nii.gz' #it is a link to '/home/bao/Personal/PhD_at_Trento/Research/ALS_Nivedita_Bao/Segmentation_CST_francesca/' + subj + '/DTI/data_brain.nii.gz' #cst_vtk_fname = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + subj + '_corticospinal_R_tvis.vtk' cst_ext_vtk_fname = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + subj + '_cst_R_tvis_ext.vtk' in_format = str(".trk") out_format = ".vtk" #input_file = cst_trk_fname #output_file = cst_vtk_fname input_file = cst_ext_trk_fname output_file = cst_ext_vtk_fname