Re: [Freesurfer] Problems with LME-Setup
Hi Jorge Thank you for your answer our question about CM. I worked so far and the results are in line with glm_fit as you predicted. If we would like to compare the groups (4th column in our qdec.table, with (responder = 1), (non-responder = 2) coded) the CM.C would be [0 0 1 0] ? We have unbalanced group sizes here 14 responder vs. 9 non-responder. Thanks for your assistance Best, Vivian ___ 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] Problems with LME-Setup
Dear FS-Experts
We examined longitudinal t1-based data and used the -long pipeline and
mri_glmfit for testing time effects.
Now for a more powerful statistical analysis we're trying to set up LME for our
data but we struggle while adapting from the tutorials cmd's.
##Problem:
We currently struggle with building the CM that compares differences in
cortical thicknes between the 2 time points and acts kind of a paired t-test.
Could any of you experts might help us setting up the correct parameters for
our analysis?
##Basics:
- 23 Pre/Post Subjects already processed through the longitudinal pipeline
- 2 time points
- Comparison of mass univariate data
Our qdec.table.dat consists of 5 columns:
1.) fsid
2.) fsid-base
3.) time
4.) group
5.) age
##Cmd History:
[Y,mri] = fs_read_Y('/Subjects/LME/lme_setup23/lh.sad23.thickness_sm10.mgh');
lhsphere = fs_read_surf('/Subjects/LME/lme_setup23/lh.sphere.reg');
lhcortex = fs_read_label('/Subjects/LME/lme_setup23/lh.cortex.label');
Qdec_total = fReadQdec('/Subjects/LME/lme_setup23/qdec.table.dat');
Qdec_fsidbase = rmQdecCol(Qdec_total,1);
sID = Qdec_fsidbase(2:end,1);
Qdec_time = rmQdecCol(Qdec_fsidbase,1);
M = Qdec2num(Qdec_time);
[Msort,Ysort,ni] = sortData(M,1,Y,sID);
X = [ones(length(Msort),1) Msort];
[theta0,residuals] = lme_mass_fit_EMinit(X,[1],Ysort,ni,lhcortex);
[regions,RgMeans] = lme_mass_RgGrow(lhsphere,residuals,theta0,lhcortex);
lhstats = lme_mass_fit_Rgw(X,[1],Ysort,ni,theta0,regions,lhsphere);
F_lhstats = lme_mass_F(lhstats,CM);
dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0);
fs_write_fstats(F_lhstats,mri,'sig.mgh','sig');
Thank you for your assistance
Vivian
___
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Re: [Freesurfer] Problems with LME-Setup
I think it is CM.C = [0 1 0 0] if you want to test if the slope is
significantly different from 0. I also would say that for a dataset with only
two time points the results of lme will not probably be very different from
what you already got from mri_glmfit. lme is designed for more complex
unbalanced longitudinal data having some subjects with more than two time
points.
Best
-Jorge
De: Vivian R. Steiger vivianroger.stei...@uzh.ch
Para: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Enviado: Domingo 29 de septiembre de 2013 7:31
Asunto: [Freesurfer] Problems with LME-Setup
Dear FS-Experts
We examined longitudinal t1-based data and used the -long pipeline and
mri_glmfit for testing time effects.
Now for a more powerful statistical analysis we're trying to set up LME for
our data but we struggle while adapting from the tutorials cmd's.
##Problem:
We currently struggle with building the CM that compares differences in
cortical thicknes between the 2 time points and acts kind of a paired t-test.
Could any of you experts might help us setting up the correct parameters for
our analysis?
##Basics:
- 23 Pre/Post Subjects already processed through the longitudinal pipeline
- 2 time points
- Comparison of mass univariate data
Our qdec.table.dat consists of 5 columns:
1.) fsid
2.) fsid-base
3.) time
4.) group
5.) age
##Cmd History:
[Y,mri] = fs_read_Y('/Subjects/LME/lme_setup23/lh.sad23.thickness_sm10.mgh');
lhsphere = fs_read_surf('/Subjects/LME/lme_setup23/lh.sphere.reg');
lhcortex = fs_read_label('/Subjects/LME/lme_setup23/lh.cortex.label');
Qdec_total = fReadQdec('/Subjects/LME/lme_setup23/qdec.table.dat');
Qdec_fsidbase = rmQdecCol(Qdec_total,1);
sID = Qdec_fsidbase(2:end,1);
Qdec_time = rmQdecCol(Qdec_fsidbase,1);
M = Qdec2num(Qdec_time);
[Msort,Ysort,ni] = sortData(M,1,Y,sID);
X = [ones(length(Msort),1) Msort];
[theta0,residuals] = lme_mass_fit_EMinit(X,[1],Ysort,ni,lhcortex);
[regions,RgMeans] = lme_mass_RgGrow(lhsphere,residuals,theta0,lhcortex);
lhstats = lme_mass_fit_Rgw(X,[1],Ysort,ni,theta0,regions,lhsphere);
F_lhstats = lme_mass_F(lhstats,CM);
dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0);
fs_write_fstats(F_lhstats,mri,'sig.mgh','sig');
Thank you for your assistance
Vivian
___
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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
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.
