|
Size: 2168
Comment:
|
Size: 2969
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Two Groups (One Factor/Two Levels), One Covariates = | [[FsgdExamples|Back to FSGD Examples]] |
| Line 3: | Line 3: |
| 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. |
~+'''Two Groups (One Factor/Two Levels), One Covariate'''+~ |
| Line 7: | Line 5: |
| === FSGD File === | This models the input as two separate planes (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 continuous factor (eg, Age) <<TableOfContents>> = FSGD File (g2v1.fsgd) = |
| Line 21: | Line 26: |
| === Regressors === | = Regressors (DODS) = |
| Line 29: | Line 34: |
| === Contrasts === | = Contrasts = |
| Line 31: | Line 36: |
| ===== 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 group.diff.mtx == |
| Line 33: | Line 45: |
| Is there a difference between groups regressing out the effect of age? | |
| Line 34: | Line 47: |
| Contrast File: g1-g2.intercept.mtx | |
| Line 39: | Line 51: |
| 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). |
| Line 43: | Line 53: |
| ===== Contrast2: ===== | == Contrast 2 group-x-age.mtx == |
| Line 45: | Line 55: |
| 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 there a difference between the group age slopes? Note: this is an interaction between group and age. Note: not possible to test with DOSS. |
| Line 49: | Line 59: |
| Contrast File: g1-g2.slope.mtx | |
| Line 54: | Line 63: |
| 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). |
| Line 58: | Line 65: |
| ===== Contrast3: ===== Null Hypothesis: does Group1 differ from Group2 in intercept or slope? |
== Contrast 3 g1g2.intercept.mtx == Null Hypothesis: does mean of group intercepts differ from 0? Is there an average main effect regressing out age? |
| Line 61: | Line 69: |
| Contrast File: g1-vs-g2.mtx {{{ 1 -1 0 0 0 0 1 -1 }}} Note: this is an F-test (and hence unsigned). ===== Contrast4 ===== Null Hypothesis: does mean of group intercepts differ from 0? Contrast File: g1g2.intercept.mtx |
|
| Line 76: | Line 73: |
| ===== Contrast5 ===== Null Hypothesis: does mean of group slopes differ from 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. |
| Line 79: | Line 77: |
| Contrast File: g1g2.intercept.mtx | == Contrast 4 g1g2.age.mtx == Null Hypothesis: does mean of group age slope differ from 0? Is there an average affect of age regressing out the effect of group? |
| Line 83: | Line 84: |
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 group.diff.mtx \ --C group-x-age.mtx \ --C g1g2.intercept.mtx \ --C g1g2.age.mtx }}} |
Two Groups (One Factor/Two Levels), One Covariate
This models the input as two separate planes (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 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 group.diff.mtx
Null Hypothesis: is there a difference between the group intercepts? Is there a difference between groups regressing out the effect of age?
1 -1 0 0
This is a t-test with Group1>Group2 being positive (red/yellow).
Contrast 2 group-x-age.mtx
Null Hypothesis: is there a difference between the group age 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 g1g2.intercept.mtx
Null Hypothesis: does mean of group intercepts differ from 0? Is there an average main effect regressing out age?
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 4 g1g2.age.mtx
Null Hypothesis: does mean of group age slope differ from 0? Is there an average affect of age regressing out the effect of group?
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 group.diff.mtx \ --C group-x-age.mtx \ --C g1g2.intercept.mtx \ --C g1g2.age.mtx