Ejemplos de Brain.add_overlay en Python

Ejemplo n.º 1

Archivo: save_B2_cwas_iq_overlap_perms.py Proyecto: czarrar/cwas-paper

scan2_surfs     = {"lh": scan2_lh, "rh": scan2_rh}
overlap_surfs   = {"lh": overlap_lh, "rh": overlap_rh}

for hemi in sw0.hemis:
    print "visualize %s" % hemi
    
    # Bring up the beauty (the underlay)
    brain = Brain(sw0.subject_id, hemi, sw0.surf, \
                  config_opts=sw0.config_opts, \
                  subjects_dir=sw0.subjects_dir)
    
    # Scan 1
    surf_data = scan1_surfs[hemi]
    if (sum(abs(surf_data)) > 0):
        # Overlay another hopeful beauty (functional overlay)
        brain.add_overlay(surf_data, name="scan1", sign=sw0.sign)
    
        # Update colorbar
        tmp = brain.overlays["scan1"]
        lut = tmp.pos_bar.lut.table.to_array()
        lut[:,0:3] = [27,158,119]
        tmp.pos_bar.lut.table = lut
        
        # Refresh
        brain.show_view("lat")
        brain.hide_colorbar()
    
    # Scan 2
    surf_data = scan2_surfs[hemi]
    if (sum(abs(surf_data)) > 0):
        # Overlay another hopeful beauty (functional overlay)

Ejemplo n.º 2

Archivo: save_x_cwas+global_overlay_pysurfer_easythresh.py Proyecto: czarrar/cwas-paper

#code.interact(local=locals())

for hemi in sw0.hemis:
    print "visualize %s" % hemi

    # Bring up the beauty (the underlay)
    brain = Brain(sw0.subject_id, hemi, sw0.surf, \
                  config_opts=sw0.config_opts, \
                  subjects_dir=sw0.subjects_dir)

    # Scan 1
    surf_data = scan1_surfs[hemi]
    if (sum(abs(surf_data)) > 0):
        print "Scan 1"
        # Overlay another hopeful beauty (functional overlay)
        brain.add_overlay(scan1_surfs[hemi], name="scan1", sign=sw0.sign)

        # Update colorbar
        tmp = brain.overlays["scan1"]
        lut = tmp.pos_bar.lut.table.to_array()
        lut[:, 0:3] = [27, 158, 119]
        tmp.pos_bar.lut.table = lut

        # Refresh
        brain.show_view("lat")
        brain.hide_colorbar()

    # Scan 2
    surf_data = scan2_surfs[hemi]
    if (sum(abs(surf_data)) > 0):
        print "Scan 2"

Ejemplo n.º 3

Archivo: C_surface_glm_vs_mdmr_meangcor.py Proyecto: czarrar/cwas-paper

    cwas_perc_surfs = {"lh": lh_cwas_perc, "rh": rh_cwas_perc}
    glm_perc_surfs  = {"lh": lh_glm_perc, "rh": rh_glm_perc}
    overlap_surfs   = {"lh": lh_overlap, "rh": rh_overlap}

    for hemi in sw0.hemis:
        print "visualize %s" % hemi
        
        # Overlap    
        brain = Brain(sw0.subject_id, hemi, sw0.surf, \
                      config_opts=sw0.config_opts, \
                      subjects_dir=sw0.subjects_dir)
    
        surf_data = overlap_surfs[hemi]
        if (sum(abs(surf_data)) > 0):
            # Overlay another hopeful beauty (functional overlay)
            brain.add_overlay(surf_data, min=sw0.min, max=sw0.max, name="glm", 
                              sign=sw0.sign)
    
            # Update colorbar
            tmp = brain.overlays["glm"]
            tmp.pos_bar.lut.table = over_lut
        
            # Refresh
            brain.show_view("lat")
            brain.hide_colorbar()
            
            #import code
            #code.interact(local=locals())
        
        brain.save_imageset("%s_%s" % (sw0.outprefix, hemi), sw0.views, 
                            'jpg', colorbar=None)
        brain.close()