Notes on How to Run Meta-Analysis

1.  ale

2.  brainNull

## B.  brainNull masked.txt 1601 172 1000 14.12892 brainNull.txt

C.  To select an ALE threshold for uncorrected p-level of 0.0001, open up the output text file (e.g., brainNull.txt), and look at the 5th column of numbers, which are the p-values. Find the p-value that is closest to 0.0001. Then look at the corresponding value in the first column of numbers. This is the ALE value, scaled up by 1,000,000; the ALE threshold is therefore this value divided by 1,000,000 (example, p. 4).

3.  ale_paper_id

A.  Same list of Talairach or MNI coordinates as in 1(A), but include a 4th column indicating paper # (numbering MUST begin with 0, not 1!) (example, p. 5).

B.  Make a separate list of coordinates of interest. These can be, e.g., local maxima in the ALE map. As in 1(A), this text file has three columns of numbers

C.  Outputs contribution of each paper to each coordinate of interest (example, p. 6).

D.  ale_paper_id FociWithPapers.txt Peaks.txt ale_paper_id.txt 111 11 14 14.12892

4.  Finding local maxima can be done in MEDx as follows.

A.  Using MEDx.

B.  Open original ALE map or resliced 32bit version (see 5(A)) into new folder.

C.  Select Toolbox à Functional à Local Min/Max

D.  Set: report top 100 (or whatever), threshold = ALE threshold selected (e.g., 2(C) above); image = ALE map.

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Sample input for program ale

8 64 21

-52 -30 0

-10 -106 6

28 26 40

22 36 32

54 -48 32

-54 -50 14

-60 -56 0

-52 -60 -14

-52 -64 -6

6 -9 56

-32 0 44

-44 -23 3

-34 -15 4

18 -7 8

34 6 5

-44 -43 28

-6 -74 31

40 -65 27

-48 -40 -21

-51 -58 6

-18 3 -19

48 -30 -26

46 -60 6

44 -20 -6

-2 -10 39

-18 33 -3

8 -3 -15

-44 -43 28

-48 -42 -22

-61 -41 -12

-51 -35 7

-22 3 -19

46 -58 6

42 -21 -1

40 -8 0

14 3 -24

-22 33 -3

-40 13 27

-6 -78 26

-28 -35 46

53 -24 29

4 -75 22

-42 -28 -21

Sample output produced by program brainNull

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3790 1286 5.28533e-06 0.999809 0.000190854

3800 966 3.97016e-06 0.999813 0.000186861

3810 877 3.60438e-06 0.999817 0.000183284

3820 848 3.48519e-06 0.99982 0.000179768

3830 795 3.26737e-06 0.999824 0.000176489

3840 790 3.24682e-06 0.999827 0.000173271

3850 729 2.99612e-06 0.99983 0.00017029

3860 708 2.90981e-06 0.999833 0.00016737

3870 790 3.24682e-06 0.999836 0.000164092

3880 2297 9.44044e-06 0.999845 0.000154674

3890 957 3.93317e-06 0.999849 0.00015074

3900 1508 6.19773e-06 0.999855 0.000144541

3910 901 3.70302e-06 0.999859 0.000140846

3920 793 3.25915e-06 0.999862 0.000137568

3930 831 3.41533e-06 0.999866 0.00013417

3940 633 2.60157e-06 0.999868 0.000131547

3950 546 2.244e-06 0.999871 0.000129342

3960 550 2.26044e-06 0.999873 0.000127077

3970 714 2.93447e-06 0.999876 0.000124097

3980 930 3.82221e-06 0.99988 0.000120282

3990 686 2.81939e-06 0.999883 0.000117481

4000 1378 5.66344e-06 0.999888 0.000111818

4010 761 3.12763e-06 0.999891 0.000108659

4020 679 2.79062e-06 0.999894 0.000105917

4030 712 2.92625e-06 0.999897 0.000102997

4040 633 2.60157e-06 0.9999 0.000100374

4050 483 1.98508e-06 0.999902 9.84073e-05

4060 503 2.06728e-06 0.999904 9.63211e-05

4070 390 1.60286e-06 0.999905 9.47118e-05

4080 469 1.92754e-06 0.999907 9.28044e-05

4090 1018 4.18388e-06 0.999911 8.85725e-05

4100 737 3.029e-06 0.999914 8.55923e-05

4110 526 2.16181e-06 0.999917 8.33869e-05

4120 604 2.48238e-06 0.999919 8.09431e-05

4130 475 1.9522e-06 0.999921 7.89762e-05

4140 449 1.84534e-06 0.999923 7.71284e-05

4150 344 1.41381e-06 0.999924 7.56979e-05

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Sample input for program ale_paper_id

-2 -80 0 0

6 -80 -18 0

16 -100 -8 0

12 -104 0 0

-28 -86 -26 0

-16 -54 -28 0

-54 -68 -14 0

-48 -56 -6 0

-42 -50 -4 1

-42 -62 -14 1

-44 -76 -18 1

-46 -36 -24 1

-54 6 0 2

-58 -26 52 2

-4 -68 24 2

30 -50 22 2

-22 -38 -20 2

6 -62 50 2

-43 11 10 3

-20 -20 10 3

-36 9 10 4

-20 -20 10 4

8 64 21 5

-52 -30 0 5

-10 -106 6 5

28 26 40 6

22 36 32 6

54 -48 32 6

-54 -50 14 7

-60 -56 0 7

-52 -60 -14 7

-52 -64 -6 7

6 -9 56 8

-32 0 44 8

18 -7 8 8

34 6 5 8

-44 -43 28 9

-6 -74 31 9

40 -65 27 9

-48 -40 -21 9

-18 3 -19 9

48 -30 -26 9

46 -60 6 9

44 -20 -6 9

-2 -10 39 9

Sample output produced by program ale_paper_id

-50 25 -6 0.0000

0 0.00000000

1 0.00000000

2 73.86647197

3 21.75920228

4 1.22757006

5 0.00000000

6 0.00000000

7 0.00000000

8 0.00000004

9 0.00553079

10 0.15524565

11 0.00000526

12 2.98597396

13 0.00000000

44 -15 -4 0.0067

0 0.00000000

1 0.00000000

2 0.29885938

3 0.00000000

4 0.00000000

5 0.00000000

6 0.00000000

7 0.00000000

8 0.00636709

9 23.42068335

10 29.09973060

11 17.92556611

12 29.24879348

13 0.00000000

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