Hi Alex
I think that Martin added the flag --qdec to mris_preproc for version
5.2. Martin, could you confirm this please?
The code for building the study design matrix X that is in the wiki is
just an example of how lme tools can be used for that purpose but the
actual instance of your code will depend on your particular Qdec
table. For instance, usually, Freesurfer's longitudinal Qdec tables
are of the form:
fsid fsid-base sID time group...
002 002_base 002 0 0
003 003_base 003 0 1
003_m6 003_base 003 0.56 1
003_m12 003_base 003 1.12 1
003_m24 003_base 003 2.2 1
005 005_base 005 0 0
005_m6 005_base 005 0.45 0
005_m12 005_base 005 1.2 0
were "fsid" is the Freesurfer's ID, "fsid-base" is the name of the
subject's specific template, sID is the subject-specific ID uniquely
identifying each subject, "time" is the time covariate and group is
the group membership covariate (there can be more covariates of
course). I suppose that you processed your longitudinal MRI scans
using a Qdec table similar to that.
You can read that Qdec table into Matlab:
Qdec = fReadQdec('qdec.table.dat');
Now you need to build your numeric design matrix X from the cell
string array Qdec to represent a specific longitudinal design. Here
you don't need the columns fsid and fsid-base in Qdec so you simply
remove them:
Qdec = rmQdecCol(Qdec,1);
Qdec = rmQdecCol(Qdec,1);
The you can grab the subject-specific ID:
sID = Qdec(:,1);
and then remove that column:
Qdec = rmQdecCol(Qdec,1);
You can now convert your cell string array Qdec to a numeric matrix:
M = Qdec2num(Qdec);
Here, the data in M is already ordered according to time for each
subject, otherwise, you can order the data using:
[M,Y,ni] = sortData(M,1,Y,sID);
where Y is the cortical thickness data matrix that you read with
fs_read_Y. Please take a look at the help of sortData. Note that
matrix M only have two columns and you need to build your design
matrix from it. In your case it is quite simple:
X = [ones(length(M),1) M M(:,1).*M(:,2)];
That is to say X contains a column of 1s (the intercept), a column
with the time covariate, a column with the group membership and a
column with the interaction term.
Now, you are ready for fitting the lme model:
stats = lme_mass_fit_vw(X,1,Y,ni,cortex);
The 1 here (second input) means that you are using a single random
effect for the intercept term which is located in column 1 of X. Then
you can test the interaction term using:
CM.C = [0 0 0 1];
F_stats = lme_mass_F(stats,CM);
and write the significance map for visualization and FDR correction in
tksurfer
fs_write_fstats(F_stats,mri,'sig.mgh','sig');
It must be recognized that some basic Matlab knowledge is required to
apply the lme tools. But the gain in flexibility for building your
design matrix and analysis is significant. As you see, the relatively
difficult part is how to get from the Qdec variable to your design
matrix X. It requires some study-specific Matlab code. Sorry, but this
is what he have at this point.
Best
-Jorge
______________________________________________________________
De: Alex Hanganu <al.hang...@yahoo.ca>
Para: FS Mailing List <Freesurfer@nmr.mgh.harvard.edu>; Jorge
Luis Bernal-Rusiel <jbernal0...@yahoo.es>
Enviado: Miércoles 5 de diciembre de 2012 18:20
Asunto: Re: [Freesurfer] Longitudinal analysis - contrast
Can you please help with this ?
Thanks in advance !
best,
Alex.
Le 05/12/2012 6:12 PM, Alex Hanganu a écrit :
> Hi Jorge,
>
> On the page presenting the
> "../fswiki/LinearMixedEffectsModels", I think there is a
> misunderstanding -
> You show the command:
>
> "mris_preproc --qdec ...."
>
> but "--qdec" is not recognized, and in the help menu of
> "mris_preproc" I don't see this flag. So I guess you meant
> the "--fsgd" flag.
>
> so, in the fsgd file, in our example, with 2 groups, and 2
> time points, would it be more correct to put the classes for
> each subject (exmpl.1) or for 2 groups (exmpl.2), or this is
> not important at this stage ?
>
> For the previous error, we found the answer, it was because
> in the qdec file, we used the "tab" between the lines. We
> changed that to "space", and it was ok.
>
> Further, after performing the step:
> [M,Y,ni] = sortData(M,2,Y,sids);
>
> we get the Error:
> File: sortData.m Line: 59 Column: 6
> Expression or statement is incorrect--possibly unbalanced (,
> {, or [.
>
> Can you please help with this?
>
> Also, in the "lme_mass_fit_vw.m" help, we saw that we need
> to create the X - ordered design matrix. Is this matrix the
> qdec file ?
>
> As we see it now, the steps that we should perform in
> Matlab, are these:
>
> [Y,mri] ...
> lhsphere ...
> lhcortex ...
> Qdec = fRead...
> Qdec = rmQdecCol...
> sids...
> Qdec = rmQdecCol...
> M = ...
> [M,Y,ni] ...
>
> lme_mass_fit_vw(M,months,Y,Group,[],OutputFileName,[],[],[])
>
> where M - should be something like '-1' '1' '1' '-1'
> months - is the column from qdec file, where is shown the
> difference between time points
> Y - is the lh.thickness_sm10.mgh file
> Group - should be the Group column from the qdec file
> [] - are showing that the default values are to be taken.
>
> But this approach doesn't seem to be entirely correct, cause
> the M (matrix) includes either the group, either the months
> (depending how we play with the command).
>
> Thank you !!
>
> Best regards,
> Alex.
>
>
> Le 05/12/2012 2:30 PM, jorge luis a écrit :
>
> > Hi Alex
> >
> > This error is likely due to the Qdec variable being empty.
> > So, nothing was read into this variable when you applied
> >
> > Qdec = fReadQdec('qdec.table.dat');
> >
> > Please check that. If you don't find a solution to this
> > then send me your Qdec table data file and I will check it
> > out.
> >
> > Best
> > -Jorge
> >
>
>
>
>
