Hi Knut
There are a few confusing things in your question post. First, it seems that your attached images are depicting p-values. We usually use -log10(pvalue) format for visualization in tksurfer. The sig.mgh file saved by lme should be in that format. However we didn't use tksurfer to build the figures for the paper you mentioned. We instead just used matlab-based geometric objects and figures. Second, for mass-univariate analyses the contrast matrix is given to lme as a matlab structure CM.C = [0 0 1 0 0 0] not a plain matrix C. Perhaps you should try first the vertex-wise lme model to ensure that all your parameters (design matrix, data matrix, contrast matrix, etc...) are right and then give it a try to the more complex spatio-temporal lme model using the same parameters.
eg.lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex);
Then you can compare the results to have a better idea about what is going on.
Best -Jorge
El Jueves 5 de diciembre de 2013 13:29, Martin Reuter mreuter@nmr.mgh.harvard.edu escribió:
Hi Jorge,
this was on the freesurfer list. Do you know what is going on ?
Best, Martin
-------- Original Message -------- Subject: [Freesurfer] Problems with longitudinal analysis Date: Wed, 4 Dec 2013 22:04:07 +0100 From: Knut J Bjuland knutjorgen@outlook.com To: freesurfer freesurfer@nmr.mgh.harvard.edu
Hi, I have used a linear mixed model for longitudinal data analysis on a
FreeSurfer 5.3, Matlab 2013b on a system with Ubuntu 12.04. I used mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh to concatenate thickness surf files, and smoothed with mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm30.mgh --fwhm-trg 30 --cortex –noreshape. I then used the same command and options in a Matlab script, as shown at http://freesurfer.net/fswiki/LinearMixedEffectsModel found in the example for mass-univariate data analyses. . I used this design matrix: interception, time, group, group*time, gender, gender*time, and I used two random effect on interception and time. I did not compare the two random effect models with one random effect model. I used this contrast vector C=[0 0 1 0 0] for these images which are included in the email. The script ran fine but when I looked at sig.mgh, it contained many visible quadrate shapes boxes even after FDR correction, and the image looks quite different than the image in the paper in Neuroimage (Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal ). Any idea what went wrong here? Thank you! Best regards, Knut Jørgen
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.
Hi Jorge
I have tried both methods. I now get image more like the one in your paper. Can you take a look at my script please? I have used fwhm at 30 mm. How did you make the figure in Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal? Can you please send me link to the matlab scripts?
Best Knut Jørgen
On 12/05/2013 08:43 PM, jorge luis wrote:
Hi Knut
There are a few confusing things in your question post. First, it seems that your attached images are depicting /p-values/. We usually use /-log10(pvalue)/ format for visualization in tksurfer. The sig.mgh file saved by lme should be in that format. However we didn't use tksurfer to build the figures for the paper you mentioned. We instead just used matlab-based geometric objects and figures. Second, for mass-univariate analyses the contrast matrix is given to lme as a matlab structure /CM.C = [0 0 1 0 0 0] /not a plain matrix C. Perhaps you should try first the vertex-wise lme model to ensure that all your parameters (design matrix, data matrix, contrast matrix, etc...) are right and then give it a try to the more complex spatio-temporal lme model using the same parameters.
eg./lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex);/
/Then you can compare the results to have a better idea about what is going on. /
/Best/ /-Jorge/
El Jueves 5 de diciembre de 2013 13:29, Martin Reuter mreuter@nmr.mgh.harvard.edu escribió:
Hi Jorge, this was on the freesurfer list. Do you know what is going on ? Best, Martin -------- Original Message -------- Subject: [Freesurfer] Problems with longitudinal analysis Date: Wed, 4 Dec 2013 22:04:07 +0100 From: Knut J Bjuland <knutjorgen@outlook.com> <mailto:knutjorgen@outlook.com> To: freesurfer <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Hi, I have used a linear mixed model for longitudinal data analysis on a FreeSurfer 5.3, Matlab 2013b on a system with Ubuntu 12.04. I used mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh to concatenate thickness surf files, and smoothed with mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm30.mgh --fwhm-trg 30 --cortex –noreshape. I then used the same command and options in a Matlab script, as shown at http://freesurfer.net/fswiki/LinearMixedEffectsModel found in the example for mass-univariate data analyses. . I used this design matrix: interception, time, group, group*time, gender, gender*time, and I used two random effect on interception and time. I did not compare the two random effect models with one random effect model. I used this contrast vector C=[0 0 1 0 0] for these images which are included in the email. The script ran fine but when I looked at sig.mgh, it contained many visible quadrate shapes boxes even after FDR correction, and the image looks quite different than the image in the paper in Neuroimage (Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal ). Any idea what went wrong here? Thank you! Best regards, Knut Jørgen 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@nmr.mgh.harvard.edu
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jorge luis -
Knut J Bjuland