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-Russiel <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
>>>
>>
>>
>>
>>
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>--
>
>Alexandru Hanganu, M.D., PhD
>Post-doc, PCAN lab, Centre de Recherche,
>Institut Universitaire de Gériatrie de Montréal
>4565, chemin Queen Mary
>Montréal, QC, CA. H3W 1W5
>Tél: +1 514 340 3540 #4280
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