Hi Jorge,

I see now:

/Y, Beta2, sided_pval/ - have the same number of columns /fstats.pval/ and /fstats.sgn/ were not generated (or they are not in the workspace) !

a.

Le 3/11 11:53, jorge luis a écrit :

Hi Alex

The cmd

/[detvtx,sided_pval,pth//] = lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);// /

only takes a few seconds to finish. Please check if /Y, Beta2, fstats.pval/,/fstats.sgn,/ /sided_pval / all have the same number of columns.

Best -Jorge

------------------------------------------------------------------------
*De:* Alex Hanganu <al.hanganu@yahoo.ca>
*Para:* Jorge L. Bernal-Rusiel <jbernal@nmr.mgh.harvard.edu>; FS
Mailing List <Freesurfer@nmr.mgh.harvard.edu>
*Enviado:* Lunes 11 de marzo de 2013 10:53
*Asunto:* [Freesurfer] LME - lme_mass_FDR2 correction doesn't work

Hi Jorge,

I got an error in the correction, and I can't find a way out.
this is the cmd I use:
-------------
/[Y,mri] = fs_read_Y('.../thickness-sm10.mgh');
Qdec = fReadQdec('.../LME.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
ni = [2 2... 2];
X = [ones(length(M),1) M M(:,1).*M(:,2)];
[stats,st] = lme_mass_fit_vw1(X,[1],Y,ni,lhcortex);
CM.C = [0 0 0 1];
fstats = lme_mass_F1(stats,CM);
fs_write_fstats(fstats,mri,'.../lh.sig.mgh','sig');
nv = length(stats);
Beta2 = zeros(1,nv);
//Beta//4////= zeros(1,nv);//
//for ....//
//.
.//
//end;
//Beta2_Beta//4//_sum = Beta2//+Beta4;//
//mri1 = mri;//
//mri1.vols//z(//4) = 1;//
//fs//_write_Y(Beta2,mri1,'..../Beta2.mgh'//);//
//[detvtx,sided_pval,pth//] =
lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);//
//fs_write_Y(sided_pva//l,mri1,//'.../spval.mgh');//
//
//??? Error using //===> reshape//
//To RESHAPE the number of elements must not change.//
//
//Error in ==//> fs_write_Y at 21//
//save_mgh(reshape(Y',mri.volsz),//fname,mri.M,mri.mr//_parms);/
-------------

the cmd: /[detvtx ....//]/ didn't work, but there was no error
message. I remember in the past this cmd took around 1 day to
analyzebut now it didn't work at all.

/fs_write_Y/ worked fine for Beta, alsothis time I used the
/mri//1 //= mri/ cmd- so the /reshape /error shouldn't be
associated with this.

Please help !

best regards,

Alex.

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Hi Alex, use the eTIV from the longitudinal subject. In theory, the size of the skull is not changing, and the longitudinal analysis gives you the best estimate of this unchanging number. doug

On 08/06/2013 06:00 PM, Alex Hanganu wrote:

Hello,

I am measuring the changes of subcortical volumes in a longitudinal study, so I took the volumes from longitudinal subjects (/name.long.base/). Now we need to perform the correction using the eTIV parameter, but the eTIV for longitudinal subjects for all time points is the same (/i//.e. eTIV for subject-time1.long.base = eTIV for subject-time2.long.base/)

Is it correct to perform the correction using the eTIV values from the longitudinal subjects, or we should use these measures from the cross-sectional corresponding subjects ?

Thanks,

Alex.

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