Differences between revisions 6 and 7
 Deletions are marked like this. Additions are marked like this. Line 1: Line 1: ~+'''Two Groups (One Factor/Two Levels), One Covariates'''+~ ~+'''Two Groups (One Factor/Two Levels), One Covariate'''+~ Line 24: Line 24: = Regressors (DODS) = = Regressors = Line 26: Line 26: Nregressors = Nclasses*(Nvariables+1) = 2*(1+1) = 4 <
> NregressorsDODS = Nclasses*(Nvariables+1) = 2*(1+1) = 4 <
> Line 41: Line 41: == Contrast 1 == == Contrast 1 (g1-g2.intercept.mtx) == Line 44: Line 44: Contrast File: g1-g2.intercept.mtx Line 51: Line 50: == Contrast 2 == == Contrast 2 (g1-g2.slope.mtx) == Line 57: Line 56: Contrast File: g1-g2.slope.mtx Line 64: Line 62: == Contrast 3 == == Contrast 3 (g1-vs-g2.mtx) == Line 67: Line 65: Contrast File: g1-vs-g2.mtx Line 75: Line 72: == Contrast 4 == == Contrast 4 (g1g2.intercept.mtx) == Line 78: Line 75: Contrast File: g1g2.intercept.mtx Line 87: Line 83: == Contrast 5 == == Contrast 5 (g1g2.slope.mtx) == Line 90: Line 86: Contrast File: g1g2.slope.mtx

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

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).

# 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

NregressorsDODS = 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 (g1-g2.intercept.mtx)

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

`1 -1 0 0`

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

## Contrast 2 (g1-g2.slope.mtx)

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

`0 0 1 -1`

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

## Contrast 3 (g1-vs-g2.mtx)

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

```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 (g1g2.intercept.mtx)

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

`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 (g1g2.slope.mtx)

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

`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```

Fsgdf1G1V (last edited 2010-09-20 15:10:27 by MartinReuter)