help > Generate Table of Means?
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Dec 7, 2020  07:12 PM | Maria Jose Pelaez Soni
Generate Table of Means?
Good afternoon, 

I want to do ROI analysis of some PET images, I upload my PET image and I add the overlay of the aal template, then in options I am able to generate a table of means. I wanted to know what does that table exactly gives me? The average intensity of each ROI? or it gives me SUVR or what it is measuring. 

Thanks
Dec 7, 2020  10:12 PM | Chris Rorden
RE: Generate Table of Means?
Lets take a practical example:
 1. Choose a background image, e.g. File/OpenStandard/spmMotor
 2. Open an atlas as an overlay, e.g. File/AddAtlas/aal
 3. Click to select the the background image (e.g. "smpMotor") as the active layer in the "Layers" panel.
 4. Choose the "Options" button in the Layers panel and choose "Generate Table of Means"
 5. An interactive table appears at the bottom. You can click on a region to move the crosshairs to the region, you can click on the table headers to sort them by the data you want. You can right click to get a text file
 

MRIcroGL 1.2.20201102+
Notes: spmMotor on aal(interpolated)
Volume Mean XYZ Structure
840 0.183 0×-46×-32 Vermis_10
1328 0.372 0×-54×-34 Vermis_9
1920 0.312 2×-64×-34 Vermis_8
1560 0.185 2×-72×-26 Vermis_7
2944 0.917 2×-68×-16 Vermis_6
5352 1.101 2×-52×-6 Vermis_4_5
1840 1.162 2×-40×-12 Vermis_3
376 -0.446 0×-38×-20 Vermis_1_2
1288 -0.441 26×-34×-42 Cerebelum_10_R
1184 -0.667 -22×-34×-42 Cerebelum_10_L
6360 0.916 10×-50×-46 Cerebelum_9_R
6832 0.325 -10×-50×-46 Cerebelum_9_L
18216 0.248 26×-56×-50 Cerebelum_8_R
15008 0.298 -26×-54×-48 Cerebelum_8_L
4192 0.608 34×-64×-46 Cerebelum_7b_R
4480 0.349 -34×-62×-44 Cerebelum_7b_L
14432 0.391 24×-58×-24 Cerebelum_6_R
13896 1.330 -24×-60×-22 Cerebelum_6_L
6456 0.375 18×-42×-18 Cerebelum_4_5_R
9120 1.700 -14×-44×-16 Cerebelum_4_5_L
1536 0.647 12×-34×-20 Cerebelum_3_R
1056 0.491 -8×-38×-18 Cerebelum_3_L
17160 0.713 32×-68×-40 Cerebelum_Crus2_R
15440 0.637 -28×-74×-38 Cerebelum_Crus2_L
20664 0.621 38×-68×-30 Cerebelum_Crus1_R
20400 0.775 -36×-66×-28 Cerebelum_Crus1_L
28472 0.279 52×-32×-22 Temporal_Inf_R
25720 0.220 -50×-28×-24 Temporal_Inf_L
9456 0.340 44×14×-32 Temporal_Pole_Mid_R
5864 0.722 -38×14×-34 Temporal_Pole_Mid_L
35752 0.503 56×-38×-2 Temporal_Mid_R
39096 0.764 -56×-34×-2 Temporal_Mid_L
10520 0.645 48×14×-16 Temporal_Pole_Sup_R
10160 0.450 -40×16×-20 Temporal_Pole_Sup_L
25576 0.767 58×-22×6 Temporal_Sup_R
18120 0.601 -54×-20×8 Temporal_Sup_L
1776 1.757 44×-18×10 Heschl_R
1792 0.341 -42×-20×10 Heschl_L
8200 0.917 12×-18×8 Thalamus_R
8448 0.449 -12×-18×8 Thalamus_L
2048 0.478 20×0×0 Pallidum_R
2160 0.375 -18×0×0 Pallidum_L
8520 0.802 26×4×2 Putamen_R
7712 0.407 -24×4×2 Putamen_L
7856 0.198 14×12×10 Caudate_R
7536 0.373 -12×12×10 Caudate_L
6672 0.940 6×-32×68 Paracentral_Lobule_R
10920 0.263 -8×-26×70 Paracentral_Lobule_L
26048 0.023 8×-56×44 Precuneus_R
28600 0.462 -8×-56×48 Precuneus_L
14104 0.617 44×-60×38 Angular_R
9176 1.241 -46×-60×36 Angular_L
15728 0.719 56×-32×34 SupraMarginal_R
9648 0.037 -56×-34×30 SupraMarginal_L
10736 1.426 46×-46×50 Parietal_Inf_R
19208 0.965 -44×-46×46 Parietal_Inf_L
17144 1.333 24×-60×62 Parietal_Sup_R
16424 0.820 -24×-60×58 Parietal_Sup_L
30768 3.050 40×-26×52 Postcentral_R
30816 -0.058 -44×-22×50 Postcentral_L
20384 0.354 32×-40×-20 Fusiform_R
18048 0.327 -32×-40×-20 Fusiform_L
7960 0.500 38×-82×-8 Occipital_Inf_R
7528 1.607 -38×-78×-8 Occipital_Inf_L
15976 0.188 36×-80×20 Occipital_Mid_R
25664 1.037 -34×-80×16 Occipital_Mid_L
11064 0.010 24×-80×30 Occipital_Sup_R
10536 0.263 -18×-84×28 Occipital_Sup_L
18568 0.393 16×-66×-4 Lingual_R
17312 0.333 -16×-68×-4 Lingual_L
11136 -0.132 12×-80×28 Cuneus_R
11992 0.035 -6×-80×28 Cuneus_L
14768 -0.255 14×-74×10 Calcarine_R
18256 0.000 -8×-78×6 Calcarine_L
1920 0.581 26×0×-18 Amygdala_R
1688 -0.017 -24×0×-18 Amygdala_L
8904 0.244 24×-16×-20 ParaHippocampal_R
7960 0.061 -22×-16×-22 ParaHippocampal_L
7608 0.290 28×-20×-10 Hippocampus_R
7456 0.354 -26×-20×-10 Hippocampus_L
2584 1.167 6×-42×22 Cingulum_Post_R
3728 0.750 -6×-42×24 Cingulum_Post_L
17080 0.929 8×-8×40 Cingulum_Mid_R
15520 0.154 -6×-16×42 Cingulum_Mid_L
10288 -0.606 8×38×16 Cingulum_Ant_R
11408 -0.517 -4×36×14 Cingulum_Ant_L
14016 0.634 38×6×2 Insula_R
15184 0.063 -36×6×4 Insula_L
5824 0.560 8×36×-18 Rectus_R
7024 0.767 -6×38×-18 Rectus_L
6880 -0.344 8×52×-6 Frontal_Mid_Orb_R
5872 0.184 -6×54×-8 Frontal_Mid_Orb_L
16792 0.147 8×50×30 Frontal_Sup_Medial_R
23640 -0.100 -6×50×30 Frontal_Sup_Medial_L
2256 -0.244 8×16×-12 Olfactory_R
2256 -0.143 -10×14×-12 Olfactory_L
18688 1.320 8×0×62 Supp_Motor_Area_R
17512 1.055 -6×4×62 Supp_Motor_Area_L
10928 0.824 52×-6×14 Rolandic_Oper_R
7928 0.033 -48×-8×14 Rolandic_Oper_L
13928 1.410 40×32×-12 Frontal_Inf_Orb_R
13808 0.872 -38×30×-12 Frontal_Inf_Orb_L
16864 1.318 50×30×14 Frontal_Inf_Tri_R
19912 0.957 -46×30×14 Frontal_Inf_Tri_L
11120 1.640 50×14×22 Frontal_Inf_Oper_R
8160 1.462 -50×12×18 Frontal_Inf_Oper_L
7984 0.932 32×52×-10 Frontal_Mid_Orb_R
7088 1.251 -32×50×-10 Frontal_Mid_Orb_L
39672 0.240 36×34×34 Frontal_Mid_R
38416 -0.098 -34×32×36 Frontal_Mid_L
7608 0.631 18×48×-14 Frontal_Sup_Orb_R
7432 0.627 -18×48×-14 Frontal_Sup_Orb_L
31568 0.354 20×30×44 Frontal_Sup_R
29232 0.019 -20×34×42 Frontal_Sup_L
27000 3.063 40×-8×52 Precentral_R
28024 -0.238 -40×-6×52 Precentral_L

In this example, the means column shows the mean intensity fo each region. You could always create a simple Matlab or Python script to get more descriptives from your image.
Dec 7, 2020  10:12 PM | Maria Jose Pelaez Soni
RE: Generate Table of Means?
Thank you so much, 

If there is not much trouble for you, could you please explain me better what do you mean with a simple matlab code to get more descriptives, or help me with a simple example of that code. 

Thank you so much again.
Dec 12, 2020  01:12 AM | Maria Jose Pelaez Soni
RE: Generate Table of Means?
Originally posted by Chris Rorden:
Lets take a practical example:
 1. Choose a background image, e.g. File/OpenStandard/spmMotor
 2. Open an atlas as an overlay, e.g. File/AddAtlas/aal
 3. Click to select the the background image (e.g. "smpMotor") as the active layer in the "Layers" panel.
 4. Choose the "Options" button in the Layers panel and choose "Generate Table of Means"
 5. An interactive table appears at the bottom. You can click on a region to move the crosshairs to the region, you can click on the table headers to sort them by the data you want. You can right click to get a text file
 

MRIcroGL 1.2.20201102+
Notes: spmMotor on aal(interpolated)
Volume Mean XYZ Structure
840 0.183 0×-46×-32 Vermis_10
1328 0.372 0×-54×-34 Vermis_9
1920 0.312 2×-64×-34 Vermis_8
1560 0.185 2×-72×-26 Vermis_7
2944 0.917 2×-68×-16 Vermis_6
5352 1.101 2×-52×-6 Vermis_4_5
1840 1.162 2×-40×-12 Vermis_3
376 -0.446 0×-38×-20 Vermis_1_2
1288 -0.441 26×-34×-42 Cerebelum_10_R
1184 -0.667 -22×-34×-42 Cerebelum_10_L
6360 0.916 10×-50×-46 Cerebelum_9_R
6832 0.325 -10×-50×-46 Cerebelum_9_L
18216 0.248 26×-56×-50 Cerebelum_8_R
15008 0.298 -26×-54×-48 Cerebelum_8_L
4192 0.608 34×-64×-46 Cerebelum_7b_R
4480 0.349 -34×-62×-44 Cerebelum_7b_L
14432 0.391 24×-58×-24 Cerebelum_6_R
13896 1.330 -24×-60×-22 Cerebelum_6_L
6456 0.375 18×-42×-18 Cerebelum_4_5_R
9120 1.700 -14×-44×-16 Cerebelum_4_5_L
1536 0.647 12×-34×-20 Cerebelum_3_R
1056 0.491 -8×-38×-18 Cerebelum_3_L
17160 0.713 32×-68×-40 Cerebelum_Crus2_R
15440 0.637 -28×-74×-38 Cerebelum_Crus2_L
20664 0.621 38×-68×-30 Cerebelum_Crus1_R
20400 0.775 -36×-66×-28 Cerebelum_Crus1_L
28472 0.279 52×-32×-22 Temporal_Inf_R
25720 0.220 -50×-28×-24 Temporal_Inf_L
9456 0.340 44×14×-32 Temporal_Pole_Mid_R
5864 0.722 -38×14×-34 Temporal_Pole_Mid_L
35752 0.503 56×-38×-2 Temporal_Mid_R
39096 0.764 -56×-34×-2 Temporal_Mid_L
10520 0.645 48×14×-16 Temporal_Pole_Sup_R
10160 0.450 -40×16×-20 Temporal_Pole_Sup_L
25576 0.767 58×-22×6 Temporal_Sup_R
18120 0.601 -54×-20×8 Temporal_Sup_L
1776 1.757 44×-18×10 Heschl_R
1792 0.341 -42×-20×10 Heschl_L
8200 0.917 12×-18×8 Thalamus_R
8448 0.449 -12×-18×8 Thalamus_L
2048 0.478 20×0×0 Pallidum_R
2160 0.375 -18×0×0 Pallidum_L
8520 0.802 26×4×2 Putamen_R
7712 0.407 -24×4×2 Putamen_L
7856 0.198 14×12×10 Caudate_R
7536 0.373 -12×12×10 Caudate_L
6672 0.940 6×-32×68 Paracentral_Lobule_R
10920 0.263 -8×-26×70 Paracentral_Lobule_L
26048 0.023 8×-56×44 Precuneus_R
28600 0.462 -8×-56×48 Precuneus_L
14104 0.617 44×-60×38 Angular_R
9176 1.241 -46×-60×36 Angular_L
15728 0.719 56×-32×34 SupraMarginal_R
9648 0.037 -56×-34×30 SupraMarginal_L
10736 1.426 46×-46×50 Parietal_Inf_R
19208 0.965 -44×-46×46 Parietal_Inf_L
17144 1.333 24×-60×62 Parietal_Sup_R
16424 0.820 -24×-60×58 Parietal_Sup_L
30768 3.050 40×-26×52 Postcentral_R
30816 -0.058 -44×-22×50 Postcentral_L
20384 0.354 32×-40×-20 Fusiform_R
18048 0.327 -32×-40×-20 Fusiform_L
7960 0.500 38×-82×-8 Occipital_Inf_R
7528 1.607 -38×-78×-8 Occipital_Inf_L
15976 0.188 36×-80×20 Occipital_Mid_R
25664 1.037 -34×-80×16 Occipital_Mid_L
11064 0.010 24×-80×30 Occipital_Sup_R
10536 0.263 -18×-84×28 Occipital_Sup_L
18568 0.393 16×-66×-4 Lingual_R
17312 0.333 -16×-68×-4 Lingual_L
11136 -0.132 12×-80×28 Cuneus_R
11992 0.035 -6×-80×28 Cuneus_L
14768 -0.255 14×-74×10 Calcarine_R
18256 0.000 -8×-78×6 Calcarine_L
1920 0.581 26×0×-18 Amygdala_R
1688 -0.017 -24×0×-18 Amygdala_L
8904 0.244 24×-16×-20 ParaHippocampal_R
7960 0.061 -22×-16×-22 ParaHippocampal_L
7608 0.290 28×-20×-10 Hippocampus_R
7456 0.354 -26×-20×-10 Hippocampus_L
2584 1.167 6×-42×22 Cingulum_Post_R
3728 0.750 -6×-42×24 Cingulum_Post_L
17080 0.929 8×-8×40 Cingulum_Mid_R
15520 0.154 -6×-16×42 Cingulum_Mid_L
10288 -0.606 8×38×16 Cingulum_Ant_R
11408 -0.517 -4×36×14 Cingulum_Ant_L
14016 0.634 38×6×2 Insula_R
15184 0.063 -36×6×4 Insula_L
5824 0.560 8×36×-18 Rectus_R
7024 0.767 -6×38×-18 Rectus_L
6880 -0.344 8×52×-6 Frontal_Mid_Orb_R
5872 0.184 -6×54×-8 Frontal_Mid_Orb_L
16792 0.147 8×50×30 Frontal_Sup_Medial_R
23640 -0.100 -6×50×30 Frontal_Sup_Medial_L
2256 -0.244 8×16×-12 Olfactory_R
2256 -0.143 -10×14×-12 Olfactory_L
18688 1.320 8×0×62 Supp_Motor_Area_R
17512 1.055 -6×4×62 Supp_Motor_Area_L
10928 0.824 52×-6×14 Rolandic_Oper_R
7928 0.033 -48×-8×14 Rolandic_Oper_L
13928 1.410 40×32×-12 Frontal_Inf_Orb_R
13808 0.872 -38×30×-12 Frontal_Inf_Orb_L
16864 1.318 50×30×14 Frontal_Inf_Tri_R
19912 0.957 -46×30×14 Frontal_Inf_Tri_L
11120 1.640 50×14×22 Frontal_Inf_Oper_R
8160 1.462 -50×12×18 Frontal_Inf_Oper_L
7984 0.932 32×52×-10 Frontal_Mid_Orb_R
7088 1.251 -32×50×-10 Frontal_Mid_Orb_L
39672 0.240 36×34×34 Frontal_Mid_R
38416 -0.098 -34×32×36 Frontal_Mid_L
7608 0.631 18×48×-14 Frontal_Sup_Orb_R
7432 0.627 -18×48×-14 Frontal_Sup_Orb_L
31568 0.354 20×30×44 Frontal_Sup_R
29232 0.019 -20×34×42 Frontal_Sup_L
27000 3.063 40×-8×52 Precentral_R
28024 -0.238 -40×-6×52 Precentral_L

In this example, the means column shows the mean intensity fo each region. You could always create a simple Matlab or Python script to get more descriptives from your image.


Thank you so much,

If there is not much trouble for you, could you please explain me better what do you mean with a simple matlab code to get more descriptives, or help me with a simple example of that code.
Thank you so much again.