Deletions are marked like this. | Additions are marked like this. |

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This models the input as two lines. If DODS, then each line has its own intercept and slope. If DOSS, then each line has its own intercept but they share a slope. |
This models the input as two separate lines (DODS), one for each group. The two groups can be thought of as two levels of a single discrete factor. The covariate can be thought of as a continuous factor (eg, Age). |

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=== FSGD File === |
<<TableOfContents>> == FSGD File (g2v1.fsgd) == |

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=== Regressors === | == Regressors (DODS) == |

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=== Contrasts === | == Contrasts == |

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===== Contrast1 ===== |
The number of columns in each contrast matrix must be the same as the number of regressors (Nregressors). If there is only one row in the contrast matrix, then the result will be a t-test and will have a sign. Reversing the signs in the contrast matrix will only change the sign of the output, not its magnitude. If there is more than one row, the result will be an F-test and will be unsigned. === Contrast 1 === |

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Since this is a t-test, the output will be signed, with Group1>Group2 being positive (red/yellow). Reversing the sign will only change the sign of the output, not its magnitude. |
This is a t-test with Group1>Group2 being positive (red/yellow). |

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===== Contrast2: ===== | === Contrast 2 === |

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Since this is a t-test, the output will be signed, with Group1>Group2 being positive (red/yellow). Reversing the sign will only change the sign of the output, not its magnitude. |
This is a t-test with Group1>Group2 being positive (red/yellow). |

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===== Contrast3: ===== | === Contrast 3 === |

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Note: this is an F-test (and hence unsigned). |
Note: this is an F-test (and hence unsigned). Reversing the signs will have no effect. |

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===== Contrast4 ===== | === Contrast 4 === |

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===== Contrast5 ===== |
This is a t-test with (Group1+Group2)/2 > 0 being positive (red/yellow). If the mean is < 0, then it will be displayed in blue/cyan. === Contrast 5 === |

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Contrast File: g1g2.intercept.mtx | Contrast File: g1g2.slope.mtx |

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This is a t-test with (Group1+Group2)/2 > 0 being positive (red/yellow). If the mean is < 0, then it will be displayed in blue/cyan. == mri_glmfit command == This is an example invocation of mri_glmfit. Depending upon your application, you may have other options as well. {{{ mri_glmfit \ --glmdir g2v1 \ --y y.mgh \ --fsgd g2v1.fsgd \ --C g1-g2.slope.mtx \ --C g1-vs-g2.mtx \ --C g1g2.intercept.mtx \ --C g1g2.slope.mtx }}} |

# Two Groups (One Factor/Two Levels), One Covariates

This models the input as two separate lines (DODS), one for each group. The two groups can be thought of as two levels of a single discrete factor. The covariate can be thought of as a continuous factor (eg, Age).

Contents

## FSGD File (g2v1.fsgd)

GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variable Age Input subject1 Group1 30 Input subject2 Group2 40

Nclasses = 2

Nvariables = 1

## Regressors (DODS)

Nregressors = Nclasses*(Nvariables+1) = 2*(1+1) = 4

Regressor1: ones for subjects in Group 1, 0 otherwise. Codes intercept/mean for Group 1

Regressor2: ones for subjects in Group 2, 0 otherwise. Codes intercept/mean for Group 2

Regressor3: age for subjects in Group 1, 0 otherwise. Codes age slope for Group 1

Regressor4: age for subjects in Group 2, 0 otherwise. Codes age slope for Group 2

## Contrasts

The number of columns in each contrast matrix must be the same as the number of regressors (Nregressors). If there is only one row in the contrast matrix, then the result will be a t-test and will have a sign. Reversing the signs in the contrast matrix will only change the sign of the output, not its magnitude. If there is more than one row, the result will be an F-test and will be unsigned.

### Contrast 1

Null Hypothesis: is there a difference between the group intercepts?

Contrast File: g1-g2.intercept.mtx

1 -1 0 0

This is a t-test with Group1>Group2 being positive (red/yellow).

### Contrast 2

Null Hypothesis: is there a difference between the group slopes? Note: this is an interaction between group and age. Note: not possible to test with DOSS

Contrast File: g1-g2.slope.mtx

0 0 1 -1

This is a t-test with Group1>Group2 being positive (red/yellow).

### Contrast 3

Null Hypothesis: does Group1 differ from Group2 in intercept or slope?

Contrast File: g1-vs-g2.mtx

1 -1 0 0 0 0 1 -1

Note: this is an F-test (and hence unsigned). Reversing the signs will have no effect.

### Contrast 4

Null Hypothesis: does mean of group intercepts differ from 0?

Contrast File: g1g2.intercept.mtx

0.5 0.5 0 0

This is a t-test with (Group1+Group2)/2 > 0 being positive (red/yellow). If the mean is < 0, then it will be displayed in blue/cyan.

### Contrast 5

Null Hypothesis: does mean of group slopes differ from 0?

Contrast File: g1g2.slope.mtx

0 0 0.5 0.5

This is a t-test with (Group1+Group2)/2 > 0 being positive (red/yellow). If the mean is < 0, then it will be displayed in blue/cyan.

## mri_glmfit command

This is an example invocation of mri_glmfit. Depending upon your application, you may have other options as well.

mri_glmfit \ --glmdir g2v1 \ --y y.mgh \ --fsgd g2v1.fsgd \ --C g1-g2.slope.mtx \ --C g1-vs-g2.mtx \ --C g1g2.intercept.mtx \ --C g1g2.slope.mtx