help > RE: Descriptives from VLSM Z map
Jul 6, 2020  01:07 PM | Chris Rorden
RE: Descriptives from VLSM Z map
If you have a statistical map loaded on top of an Atlas, you can use this procedure
 1.) Load the Atlas as your background image:
       Choose File/AddAtlas/aal while holding down the CONTROL key (reversing standard behavior of opening atlases as overlays)
 2.) Add your statistlcal map as an overlay
      a.  Choose File/AddOverlay to select your own map
      b. ALTERNATIVELY, for a demo you can force the map spmMotor to be added as an overlay by selecting File/OpenStandard/spmMotor while holding down the CONTROL key (reversing default behavior of loading ordinary images as backgrounds)
 3.) In the Layers menu, set the "Darkest" and "Brightest" values to threshold your overlay. For the example lets set this to 2 and 4 (to hide voxels darker than t(262)=2.0.
 4.) In the Layer menu with your statistical map selected, press the "Options" button and choose "Generate Cluster Table"

An interactive cluster table appears at the bottom. You can click on a cluster to see the location, you can click on the cluster table header to sort by volume (cc), Peak, or structure name. You can right click on the table to save to your clipboard:

MRIcroGL 1.2.20200707
Notes: spmMotor(interpolated) on aal
Volume Peak • PeakXYZ Peak Structure XYZ Structure
76 2.4 8×58×30 Frontal_Sup_Medial_R 10×58×29 Frontal_Sup_Medial_R(95) Frontal_Sup_R(5)
3866 3.6 6×28×50 Frontal_Sup_Medial_R -1×25×50 Supp_Motor_Area_L(42) Frontal_Sup_Medial_L(19) Frontal_Sup_Medial_R(18) Supp_Motor_Area_R(17) Frontal_Sup_L(2) Cingulum_Mid_R(1) Cingulum_Mid_L(1)
67 2.3 6×-46×26 Cingulum_Post_R 6×-46×26 Cingulum_Post_R(99) Precuneus_R(1)
51 2.2 66×-2×22 Postcentral_R 65×-2×22 Postcentral_R(100)
2448 3.3 64×-44×24 Temporal_Sup_R 64×-39×21 Temporal_Sup_R(61) SupraMarginal_R(20) Angular_R(19)
272 2.8 64×-42×2 Temporal_Mid_R 65×-41×2 Temporal_Mid_R(100)
114 2.3 54×-30×-10 Temporal_Mid_R 54×-29×-10 Temporal_Mid_R(96) -(4)
48 2.4 50×-60×12 Temporal_Mid_R 51×-61×11 Temporal_Mid_R(100)
43 2.2 50×-36×28 SupraMarginal_R 51×-37×26 SupraMarginal_R(95) Temporal_Sup_R(5)
234 2.4 4×-34×70 Paracentral_Lobule_R 4×-34×69 Paracentral_Lobule_R(100)
5739 4.3 48×48×-12 Frontal_Inf_Orb_R 42×40×-9 Frontal_Inf_Orb_R(57) Frontal_Mid_Orb_R(17) -(11) Frontal_Inf_Tri_R(9) Insula_R(5)
1937 3.4 48×-68×-2 Temporal_Inf_R 47×-69×-3 Temporal_Inf_R(37) Temporal_Mid_R(34) Occipital_Inf_R(15) -(7) Occipital_Mid_R(5) Fusiform_R(2) Cerebelum_Crus1_R(1)
69000 12.2 48×-14×56 Precentral_R 33×-14×51 Postcentral_R(24) Precentral_R(20) -(9) Frontal_Inf_Tri_R(7) Supp_Motor_Area_R(6) Parietal_Sup_R(6) Frontal_Inf_Oper_R(6) Frontal_Mid_R(5) Cingulum_Mid_R(4) Frontal_Sup_R(4) Parietal_Inf_R(4) Supp_Motor_Area_L(2) Precuneus_R(1) Paracentral_Lobule_L
42 2.3 42×-24×-10 42×-24×-9 -(71) Hippocampus_R(29)
6162 4.3 38×-14×16 Insula_R 40×-13×8 Insula_R(21) Rolandic_Oper_R(19) Temporal_Sup_R(15) -(13) Heschl_R(12) Thalamus_R(11) Putamen_R(9) Postcentral_R(1)
1538 3.3 36×-82×-46 37×-78×-42 Cerebelum_Crus2_R(76) Cerebelum_Crus1_R(14) -(7) Cerebelum_7b_R(3)
36 2.2 36×-78×18 Occipital_Mid_R 37×-79×16 Occipital_Mid_R(100)
1404 3.3 34×-58×-26 Cerebelum_6_R 34×-59×-24 Cerebelum_6_R(68) Fusiform_R(19) Cerebelum_Crus1_R(13)
737 2.9 22×24×-22 Frontal_Inf_Orb_R 18×27×-21 Frontal_Inf_Orb_R(45) Frontal_Sup_Orb_R(38) Rectus_R(17)
940 3.3 18×-82×-26 Cerebelum_Crus1_R 18×-82×-28 Cerebelum_Crus1_R(79) Cerebelum_Crus2_R(21)
65 2.4 14×58×-22 Frontal_Sup_Orb_R 13×58×-22 Frontal_Sup_Orb_R(77) -(23)
123 2.4 10×2×16 Caudate_R 9×2×14 Caudate_R(61) -(39)
1341 3.6 10×-44×-46 Cerebelum_9_R 5×-52×-45 Cerebelum_9_R(68) Cerebelum_9_L(12) -(9) Cerebelum_8_L(6) Vermis_9(6)
940 2.9 0×28×-28 -1×32×-27 -(70) Rectus_L(16) Rectus_R(11) Frontal_Sup_Orb_L(3)
837 3.7 -6×62×-24 -6×64×-16 Frontal_Mid_Orb_L(34) Rectus_L(30) -(22) Frontal_Sup_Orb_L(14)
153 2.9 -6×-80×-44 -5×-79×-44 -(97) Cerebelum_Crus2_L(3)
45 2.5 -68×-12×16 -67×-12×13 -(64) Postcentral_L(27) Temporal_Sup_L(9)
182 2.5 -60×12×-6 -59×11×-5 Temporal_Pole_Sup_L(70) -(29) Rolandic_Oper_L(1)
2627 3.4 -60×-38×-4 Temporal_Mid_L -62×-40×-3 Temporal_Mid_L(97) Temporal_Inf_L(3)
69 2.5 -54×-18×46 Postcentral_L -54×-17×47 Postcentral_L(100)
119 2.4 -42×2×-44 -43×2×-42 -(62) Temporal_Inf_L(38)
4673 3.5 -38×56×-4 Frontal_Mid_Orb_L -43×47×-7 Frontal_Mid_Orb_L(43) Frontal_Inf_Orb_L(38) -(14) Frontal_Mid_L(4) Frontal_Sup_Orb_L(1) Frontal_Inf_Tri_L(1)
488 3.3 -36×-32×42 Postcentral_L -37×-33×44 Postcentral_L(66) Parietal_Inf_L(29) -(5)
334 2.8 -34×22×-4 Insula_L -35×22×-4 Insula_L(87) Frontal_Inf_Orb_L(11) Frontal_Inf_Tri_L(2)
469 3.1 -34×18×-30 Temporal_Pole_Sup_L -35×16×-29 Temporal_Pole_Sup_L(67) Temporal_Pole_Mid_L(33)
4651 3.7 -34×-60×36 Angular_L -43×-57×40 Angular_L(43) Parietal_Inf_L(40) Occipital_Mid_L(8) Parietal_Sup_L(5) SupraMarginal_L(3) -(2)
187 2.6 -32×-66×-48 Cerebelum_7b_L -33×-66×-48 Cerebelum_7b_L(56) Cerebelum_8_L(34) Cerebelum_Crus2_L(10)
76 2.4 -32×-28×0 -32×-27×-1 -(96) Hippocampus_L(4)
8101 4.1 -30×8×60 Frontal_Mid_L -43×13×35 Frontal_Mid_L(28) Frontal_Inf_Tri_L(25) Frontal_Inf_Oper_L(24) Precentral_L(22) -(1) Postcentral_L(1)
78 2.7 -30×4×-26 -31×4×-26 -(86) Amygdala_L(10) Temporal_Pole_Sup_L(3) ParaHippocampal_L(1)
132 2.6 -2×-36×-46 -2×-38×-46 -(100)
214 2.3 -26×-78×42 Occipital_Mid_L -25×-77×43 Occipital_Sup_L(39) Parietal_Sup_L(36) Occipital_Mid_L(25)
166 2.5 -26×-6×44 -25×-6×45 -(96) Precentral_L(3) Frontal_Sup_L(1)
141 2.4 -24×-76×24 Occipital_Sup_L -25×-76×24 Occipital_Mid_L(48) Occipital_Sup_L(36) -(16)
33 2.4 -24×-56×-48 Cerebelum_8_L -24×-55×-48 Cerebelum_8_L(100)
29135 5.5 -24×-50×-22 Cerebelum_6_L -17×-60×-6 Occipital_Mid_L(16) Cerebelum_6_L(13) Cerebelum_4_5_L(13) -(13) Cerebelum_Crus1_L(8) Occipital_Inf_L(7) Lingual_R(5) Vermis_4_5(5) Cerebelum_4_5_R(2) Vermis_6(2) Vermis_3(2) Precuneus_R(2) Lingual_L(2) Thalamus_R(1) Fusiform_L(1) Thalamus_L(1) Cing
239 2.6 -20×62×-6 Frontal_Sup_Orb_L -19×64×-4 Frontal_Sup_Orb_L(82) Frontal_Mid_Orb_L(10) Frontal_Sup_Medial_L(7) Frontal_Mid_Orb_L(2)
88 2.4 -20×-6×54 -19×-6×54 -(93) Frontal_Sup_L(7)
111 2.3 -18×52×32 Frontal_Sup_L -18×53×32 Frontal_Sup_L(92) Frontal_Mid_L(8)
374 2.8 -14×16×2 Caudate_L -13×16×1 Caudate_L(65) -(20) Putamen_L(15)
4345 4.6 -14×-62×68 Precuneus_L -15×-55×65 Precuneus_L(63) Parietal_Sup_L(36) -(1)
88 2.6 -10×24×-14 Rectus_L -10×24×-14 Rectus_L(100)
42 2.2 -10×-46×26 Cingulum_Post_L -10×-47×25 Cingulum_Post_L(95) Precuneus_L(5)
42 2.2 -10×-22×30 -11×-22×30 -(100)


Alternatively, you could load an anatomical image as your background layer
1.) Load your background image:
 Choose File/AddStandard/spm152
2.) Load the Atlas as an overlay image:
  Choose File/AddAtlas/aal 
3.) Add your statistlcal map as an overlay
  a. Choose File/AddOverlay to select your own map
  b. ALTERNATIVELY, for a demo you can force the map spmMotor to be added as an overlay by selecting File/OpenStandard/spmMotor while holding down the CONTROL key (reversing default behavior of loading ordinary images as backgrounds)
4.) In the Layers menu, set the "Darkest" and "Brightest" values to threshold your overlay. For the example lets set this to 2 and 4 (to hide voxels darker than t(262)=2.0.
5.) In the Layer menu with your statistical map selected, press the "Options" button and choose "Generate Cluster Table"

The script below automates steps 1..4:

import gl
gl.resetdefaults()
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('aal')
gl.scriptformvisible(1)
gl.overlayload('spmMotor')
gl.minmax(2, 4, 4)
Attachment: cluster_table.png

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TitleAuthorDate
Noelia Martinez Molina Jun 4, 2020
Natalia Ladyka-Wojcik Oct 16, 2023
RE: Descriptives from VLSM Z map
Chris Rorden Jul 6, 2020
William Mccuddy Jun 19, 2020