Yes,
in 5.2 there should be the two new options --qdec and --qdec-long
to allow passing qdec tables both in the regular cross sectional and in
the longitudinal format in addition to the existing other ways of
passing subjects lists (--s or --fsgd or --f ).
Now care needs to be taken in the longitudinal setting. What you want is
to get the files (e.g. thickness) from the *.long.<base> directories
into the target (e.g fsaverage space). Not from the cross sectional
directories!
For this you will be able to use the longitudinal qdec file (with a
column of 'fsid' and 'fsid-base' to group time points into subjects, see
wiki).
In 5.1 you should do the following:
create a text file with each longitudinal id (containing
the .long.<base> ) per line and pass it using the --f flag.
So in the example below you'd write:
002.long.002_base
003.long.003_base
003_m6.long.003_base
You can use a simple shell command to get such a list from a
longitudinal qdec file:
cat long.qdec.table.txt | awk '{if ($1 != "fsid" && substr($1,0,1) !=
"#") printf("%s.long.%s\n", $1, $2)}' > outsubjectsfile.txt
Then preproc will do its job. The order of subjects needs to be
identical to the qdec file that you use to run the LME matlab tools to
ensure thickenss maps are stacked in the same order as you pass the
covariates.
Best, Martin
On Thu, 2012-12-06 at 04:27 +0000, jorge luis wrote:
> 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
> > >
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to
> whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> > contains patient information, please contact the Partners
> Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> > but does not contain patient information, please contact the sender
> and properly
> > dispose of the e-mail.
>
>
> --
> 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
> Portable: +1 514 441 9159
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person
> to whom it is
> addressed. If you believe this e-mail was sent to you in error
> and the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was
> sent to you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
