|
Size: 2967
Comment:
|
Size: 1695
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| ~+'''Two Groups (One Factor/Two Levels), One Covariate'''+~ | [[FsgdExamples|Back to FSGD Examples]] |
| Line 3: | Line 3: |
| 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). |
~+'''One Group, One Covariate'''+~ This models the input as a single line (ie, an intercept and a slope). factor (eg, Age). Because there is only one group, this will be the same for both DODS and DOSS. |
| Line 10: | Line 11: |
| = FSGD File (g2v1.fsgd) = | = FSGD File (g1v1.fsgd) = |
| Line 14: | Line 15: |
| Class Group1 Class Group2 |
Class Main |
| Line 17: | Line 17: |
| Input subject1 Group1 30 Input subject2 Group2 40 |
Input subject1 Main 30 Input subject2 Main 40 |
| Line 21: | Line 21: |
| Nclasses = 2 <<BR>> | Nclasses = 1 <<BR>> |
| Line 26: | Line 26: |
| NregressorsDODS = 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>> |
| Line 41: | Line 39: |
| == Contrast 1 (g1-g2.intercept.mtx) == Null Hypothesis: is there a difference between the group intercepts? |
== Contrast 1 (intercept.mtx) == Null Hypothesis: is the intercept equal to 0? |
| Line 45: | Line 43: |
| 1 -1 0 0 | 1 0 |
| Line 48: | Line 46: |
| 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). |
| Line 50: | Line 48: |
| == Contrast 2 (g1-g2.slope.mtx) == | == Contrast 2 (slope.mtx) == |
| Line 52: | Line 50: |
| 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? |
| Line 57: | Line 53: |
| 0 0 1 -1 | 0 1 |
| Line 60: | Line 56: |
| 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. |
This is a t-test with the slope>0 being positive (red/yellow). |
| Line 101: | Line 65: |
| --glmdir g2v1 \ | --glmdir g1v1 \ |
| Line 103: | Line 67: |
| --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 |
One Group, One Covariate
This models the input as a single line (ie, an intercept and a slope). factor (eg, Age). Because there is only one group, this will be the same for both DODS and DOSS.
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