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← Revision 13 as of 2026-06-11 16:59:50 ⇥
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| ~+'''Two Groups (One Factor/Two Levels), One Covariate'''+~ | [[FsgdExamples|Back to FSGD Examples]] |
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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 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. |
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| = FSGD File (g2v1.fsgd) = | = FSGD File (g1v1.fsgd) = |
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| Class Group1 Class Group2 Variable Age Input subject1 Group1 30 Input subject2 Group2 40 |
Class Main Contrast intercept 1 0 Contrast slope 0 1 Variables Age Input subject1 Main 30 Input subject2 Main 40 |
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| Nclasses = 2 <<BR>> | Nclasses = 1 <<BR>> |
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| 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>> |
NregressorsDODS = Nclasses*(Nvariables+1) = 1*(1+1) = 2 <<BR>> NregressorsDOSS = Nclassesd + Nvariables = 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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| == Contrast 1 (g1-g2.intercept.mtx) == Null Hypothesis: is there a difference between the group intercepts? |
= mri_glmfit command = This is an example invocation of mri_glmfit. Depending upon your application, you may have other options as well. |
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| 1 -1 0 0 | mri_glmfit \ --glmdir g1v1 \ --y y.mgh \ --fsgd g1v1.fsgd \ |
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| This is a t-test with Group1>Group2 being positive (red/yellow). | Above, contrasts were embedded in the FSGD, which is convenient. You can also create contrast files as below. Note if contrasts are specified in the FSGD file, then you cannot pass them on the command line. It is either one or the other |
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| == 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 |
== Contrast 1 (intercept.mtx) == Null Hypothesis: is the intercept equal to 0? |
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| 0 0 1 -1 | 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 3 (g1-vs-g2.mtx) == Null Hypothesis: does Group1 differ from Group2 in intercept or slope? |
== Contrast 2 (slope.mtx) == Null Hypothesis: is the slope equal to 0? |
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| 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 |
0 1 |
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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. == 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). |
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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 |
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 Contrast intercept 1 0 Contrast slope 0 1 Variables Age Input subject1 Main 30 Input subject2 Main 40
Nclasses = 1
Nvariables = 1
Regressors
NregressorsDODS = Nclasses*(Nvariables+1) = 1*(1+1) = 2
NregressorsDOSS = Nclassesd + Nvariables = 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.
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 \
Above, contrasts were embedded in the FSGD, which is convenient. You can also create contrast files as below. Note if contrasts are specified in the FSGD file, then you cannot pass them on the command line. It is either one or the other
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