Hi Alex
Sorry, my bad. You are right. To grab the subjects'ID the correct code is:
sID = Qdec(2:end,1);
I'm going to fix that in the wiki. The new error is due to the numeric value on
the left hand side of
[M,Y,144] = sortData(M,1,Y,sID);
You cannot assign any value to 144. Just change that code by this:
[M,Y,ni] = sortData(M,1,Y,sID);
and use ni instead of 144 everywhere. Note that ni must be a vector of the
same size as the number of subjects in your study (36), not a single numeric
value.
Best
-Jorge
>________________________________
> De: Alex Hanganu <al.hang...@yahoo.ca>
>Para: Martin Reuter <mreu...@nmr.mgh.harvard.edu>
>CC: FS Mailing List <Freesurfer@nmr.mgh.harvard.edu>; Jorge Luis Bernal-Rusiel
><jbernal0...@yahoo.es>
>Enviado: Jueves 6 de diciembre de 2012 16:45
>Asunto: Re: Re: [Freesurfer] Longitudinal analysis - contrast
>
>
>Hello Martin,
>
>Thanks for your confirmation. I downloaded the last version of
FreeSurfer: the dev5-20120624, from the "..fswiki/LMEModels" page,
but there is the old mris_preproc, so I will use the fsgd file.
>
>Thanks for pointing out about the long.base - files!! That was a
mistake of mine. And thanks for the shell command line !
>So the fsgd file was created only with long subjects, then I created the
>lh.thickness_sm10.mgh file and went further ! OK.
>=======================
>
>
>Hi Jorge,
>
>Thanks for showing clearly the steps ! Everything went fine. The X
contains those columns as you said.
>our stats command is:
>
>stats = lme_mass_fit_vw(X,1,Y,144,cortex);
>
>where "144" is the 2*ones. We have 36 subjects and 2 time points, so we have
>72 ones * 2 -> 144. (but I also tried with 72, 36, 2)
>
>Unfortunately, there is again an error:
>
>File: lme_mass_fit.m Line: 162 Column: 14
>The variable stats in a parfor cannot be classified.
>Error in ==> lme_mass_fit_vw at 73
>[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
>
>Also when applying:
>[M,Y,144] = sortData(M,1,Y,sID);
>there is an error:An array for multiple LHS assignment cannot contain numeric
>value.
>
>Our M contains: <72x2 double> value
>The X: <72x4 double> value
>but the sID contains: <73x1 cell>
>
>so we thought that might be the problem and we removed the cell
"sID" , and we got and sID: <72x1 cell>. The error
persisted.
>
>did we miss something ?
>
>Thank you !
>
>Sincerely,
>Alex.
>
>
>
>
>
>Le 06/12/2012 11:15 AM, Martin Reuter a écrit :
>
>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 mailto:al.hang...@yahoo.ca Para: FS Mailing List
mailto:Freesurfer@nmr.mgh.harvard.edu; Jorge Luis Bernal-Rusiel
mailto: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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