def looping((sub, hemi, sess)):
    
    print 'running', sub, hemi, sess
    label_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/labels/%s_%s_highres2lowres_labels.npy'%(sub, hemi)
    rest_file = '/scr/ilz3/myelinconnect/resting/final/%s_rest%s_denoised.nii.gz'%(sub, sess)
    highres_file = '/scr/ilz3/myelinconnect/struct/surf_%s/orig2func/rest%s/%s_%s_mid_groupavgsurf.vtk'%(hemi, sess, sub, hemi)
        
    data_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/rest/%s_%s_rest%s_smooth_3.npy'%(sub, hemi, sess)

    # load data
    labels = np.load(label_file)[:,1]
    highres_v, highres_f, highres_d = read_vtk(highres_file)
    
    # sample resting state time series on highres mesh
    rest_highres = sample_volume(rest_file, highres_v)
    
    # average across highres vertices that map to the same lowres vertex
    rest_lowres = sample_simple(rest_highres, labels)

    # save data
    np.save(data_file, rest_lowres)
    
    if os.path.isfile(data_file):
        print sub+' '+hemi+' ' +sess+' finished'

    return data_file
def looping((sub, hemi)):

    highres_file = '/scr/ilz3/myelinconnect/struct/surf_%s/prep_t1/profiles/%s_%s_mid_proflies.vtk'%(hemi, sub, hemi)
    label_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/labels/%s_%s_highres2lowres_labels.npy'%(sub, hemi)
    old_lowres_file = '/scr/ilz3/myelinconnect/groupavg/indv_space/%s/lowres_%s_d_def.vtk'%(sub, hemi)

    
    new_lowres_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/t1/raw/%s_%s_profiles_raw.vtk'%(sub, hemi)
    data_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/t1/raw/%s_%s_profiles_raw.npy'%(sub, hemi)
    cheb_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/t1/raw/%s_%s_coeff_raw.npy'%(sub, hemi)
    cheb_vtk_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/t1/raw/%s_%s_coeff_raw.vtk'%(sub, hemi)


    # load data
    labels = np.load(label_file)[:,1]
    highres_v, highres_f, highres_d = read_vtk(highres_file)
    lowres_v, lowres_f, lowres_d = read_vtk(old_lowres_file)

    # call to sampling function
    new_lowres_d = sample_simple(highres_d, labels)

    # save lowres vtk and txt
    write_vtk(new_lowres_file, lowres_v, lowres_f, data=new_lowres_d)
    np.save(data_file, new_lowres_d)
    
    # calculate chebychev coefficients
    t1_3_7 = new_lowres_d[:,3:8]
    coeff, poly = chebapprox(t1_3_7, degree=4)
    np.save(cheb_file, coeff)
    write_vtk(cheb_vtk_file, lowres_v, lowres_f, data=coeff)
    
    if os.path.isfile(data_file):
        print sub+' '+hemi+' finished'

    return
Esempio n. 3
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def looping((sub, hemi)):

    highres_file = '/scr/ilz3/myelinconnect/struct/surf_%s/prep_t1/profiles/%s_%s_mid_proflies.vtk'%(hemi, sub, hemi)
    label_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/labels/%s_%s_highres2lowres_labels.npy'%(sub, hemi)
    old_lowres_file = '/scr/ilz3/myelinconnect/groupavg/indv_space/%s/lowres_%s_d_def.vtk'%(sub, hemi)

    
    new_lowres_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/t1/%s_%s_profiles.vtk'%(sub, hemi)
    data_file = '/scr/ilz3/myelinconnect/all_data_on_simple_surf/t1/%s_%s_profiles.npy'%(sub, hemi)


    # load data
    labels = np.load(label_file)[:,1]
    highres_v, highres_f, highres_d = read_vtk(highres_file)
    lowres_v, lowres_f, lowres_d = read_vtk(old_lowres_file)

    # call to sampling function
    new_lowres_d = sample_simple(highres_d, labels)

    # save lowres vtk and txt
    #write_vtk(new_lowres_file, lowres_v, lowres_f, data=new_lowres_d)
    np.save(data_file, new_lowres_d)
    
    if os.path.isfile(data_file):
        print sub+' '+hemi+' finished'

    return
Esempio n. 4
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for hemi in hemis:
    
    n_vertices = np.load(label_file%(subjects[0], hemi))[:,1].max()+1
    tsnr = np.zeros((n_vertices, len(subjects)*len(sessions)))
    inv2prob = np.zeros((n_vertices, len(subjects)))

    inv2prob_count = 0
    tsnr_count = 0
    for sub in subjects: 
        
        labels = np.load(label_file%(sub, hemi))[:,1]
        inv2prob_highres_v, inv2prob_highres_f, inv2prob_highres_d = read_vtk(inv2prob_highres_file%(sub, hemi))
        
        # average across highres vertices that map to the same lowres vertex
        inv2prob[:,inv2prob_count] = np.squeeze(sample_simple(inv2prob_highres_d, labels))
        
        inv2prob_count += 1
        
        for sess in sessions:
             
            print sub, sess
             
            highres_func_v, highres_func_f, highres_func_d = read_vtk(highres_func_file%(hemi, sess, sub, hemi))
              
            # sample resting state time series on highres mesh
            tsnr_highres = sample_volume(tsnr_file%(sub, sess, sub, sess), highres_func_v)
                 
            # average across highres vertices that map to the same lowres vertex
            tsnr[:,tsnr_count] = np.squeeze(sample_simple(tsnr_highres[:,np.newaxis], labels))