[[FsgdExamples|Back to FSGD Examples]]

~+'''Three Groups (One Factor/Three Levels), No Covariates'''+~

This models the input as three separate offsets/intercepts/means, one
for each group. The two groups can be thought of as three levels of a
single discrete factor (eg, Normal, Mild Cognitive Impairment (MCI),
and AD). There is not continuous covariate. These results hold for
DODS or DOSS.

<<TableOfContents>>

= FSGD File (g3v0.fsgd) =
{{{
GroupDescriptorFile 1
Title OSGM
Class Normal
Class MCI
Class AD
Input subject1 Normal
Input subject2 MCI
Input subject3 AD
}}}

Nclasses = 3 <<BR>>
Nvariables = 0 <<BR>>

= Regressors =

NregressorsDODS = Nclasses*(Nvariables+1) = 3*(0+1) = 3 <<BR>>
NregressorsDOSS = Nclasses + Nvariables = 3+0 = 3 <<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>>
Regressor2: ones for subjects in Group 3, 0 otherwise. Codes intercept/mean for Group 3 <<BR>>

= 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 normal-mci.mtx ==
Null Hypothesis: is there a difference between the normals and MCI means?

{{{
1 -1 0
}}}

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

== Contrast 2 normal-ad.mtx ==
Null Hypothesis: is there a difference between the normals and AD means?

{{{
1 0 -1
}}}

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

== Contrast 3 mci-ad.mtx ==
Null Hypothesis: is there a difference between the MCI and AD means?

{{{
0 1 -1
}}}

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

== Contrast 4 group.effect.mtx ==
Null Hypothesis: is there a difference between any of the group means?
Is there an effect of group (diagnosis)?

{{{
1 -1 0
1 0 -1
}}}

This is a F-test and so unsigned. The contrast matrix is constructed
from the contrast matrices testing Normals-vs-MCI and
Normals-vs-AD. Note that one does NOT include a third row for
MCI-vs-AD. This is because if Normals==MCI AND Normals==AD, then it
MUST be the case that MCI==AD. Inclusion of the third row will
actually cause an error.

== Contrast 5 normal+mci-vs-ad.mtx ==

Null Hypothesis: does the average of Normal and MCI equal AD?

{{{
0.5 0.5 -1
}}}

This is a t-test with Group1>Group2 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 g3v0 \
  --y y.mgh \
  --fsgd g3v0.fsgd \
  --C normal-mci.mtx \ 
  --C normal-ad.mtx \ 
  --C mci-ad.mtx  \ 
  --C group.effect.mtx \ 
  --C normal+mci-vs-ad.mtx

}}}