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= Two Groups (One Factor/Two Levels), One Covariates = | ~+'''Two Groups (One Factor/Two Levels), One Covariate'''+~ |

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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 |
This models the input as a single line (ie, an intercept and a slope). |

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=== FSGD File (g2v1.fsgd) === |
<<TableOfContents>> = FSGD File (g1v1.fsgd) = |

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Class Group1 Class Group2 |
Class Main |

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Input subject1 Group1 30 Input subject2 Group2 40 |
Input subject1 Main 30 Input subject2 Main 40 |

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Nclasses = 2 <<BR>> | Nclasses = 1 <<BR>> |

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

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Nregressors = Nclasses*(Nvariables+1) = 2*(1+1) = 4 <<BR>> Regressor1: ones for subjects in Group 1, 0 otherwise. Codes intercept/mean for Group 1 <<BR>> Regressor2: ones for subjects in Group 2, 0 otherwise. Codes intercept/mean for Group 2 <<BR>> Regressor3: age for subjects in Group 1, 0 otherwise. Codes age slope for Group 1 <<BR>> Regressor4: age for subjects in Group 2, 0 otherwise. Codes age slope for Group 2 <<BR>> |
Nregressors = Nclasses*(Nvariables+1) = 1*(1+1) = 2 <<BR>> Regressor1: All ones. Codes intercept/mean for Main <<BR>> Regressor2: age for each subject. Codes age slope for Group 1 <<BR>> |

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

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===== Contrast 1 ===== Null Hypothesis: is there a difference between the group intercepts? Is there a difference between groups regressing out the effect of age? |
== Contrast 1 (intercept.mtx) == Null Hypothesis: is the intercept equal to 0? |

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Contrast File: g1-g2.intercept.mtx | |

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1 -1 0 0 | 1 0 |

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This is a t-test with Group1>Group2 being positive (red/yellow). | This is a t-test with the intercept>0 being positive (red/yellow). |

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===== Contrast 2 ===== | == Contrast 2 (slope.mtx) == |

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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. |
Null Hypothesis: is the slope equal to 0? |

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Contrast File: g1-g2.slope.mtx | |

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0 0 1 -1 | 0 1 |

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This is a t-test with Group1>Group2 being positive (red/yellow). | This is a t-test with the slope>0 being positive (red/yellow). |

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===== 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? Is there an average affect of age regressing out the effect of group? 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 === |
= mri_glmfit command = |

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--glmdir g2v1 \ | --glmdir g1v1 \ |

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--fsgd g2v1.fsgd \ --C g1-g2.slope.mtx \ --C g1-vs-g2.mtx \ --C g1g2.intercept.mtx \ --C g1g2.slope.mtx |
--fsgd g1v1.fsgd \ --C intercept.mtx \ --C slope.mtx |

**Two Groups (One Factor/Two Levels), One Covariate**

This models the input as a single line (ie, an intercept and a slope). factor (eg, Age).

Contents

# FSGD File (g1v1.fsgd)

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

Nclasses = 1

Nvariables = 1

# Regressors

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

Regressor1: All ones. Codes intercept/mean for Main

Regressor2: age for each subject. Codes age slope for Group 1

# 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 (intercept.mtx)

Null Hypothesis: is the intercept equal to 0?

1 0

This is a t-test with the intercept>0 being positive (red/yellow).

## Contrast 2 (slope.mtx)

Null Hypothesis: is the slope equal to 0?

0 1

This is a t-test with the slope>0 being positive (red/yellow).

# 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 g1v1 \ --y y.mgh \ --fsgd g1v1.fsgd \ --C intercept.mtx \ --C slope.mtx