[Freesurfer] the Configure Overlay Display dialog is clipped on low resolution monitors.
Dear Freesurfer developers, the Configure Overlay Display dialog is clipped on low resolution monitors with FS version 5.3.0 for MAC. This bug affected the version 5.1.0 and you released a fix for it, but now it's not available anymore on the website. Best regards Cico Cardinale___ 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] Effects of age on different parameters (thickness, lGI...)
Dear FreeSurfer experts, thanks a lot for your solution. It works fine. I have some further questions to polynomial fitting with qdec, to prevent misunderstandings from my point of view. Only to be sure: 1) Linear effects of age: age as continuus factor. 2) Quadratic effects of age: age (quadratic) as continuus factor and age (linear) as nuisance factor. 3) Cubic effects of age: age (cubic) as continuus factor and age (linear) as nuisance factor. 4) Linear+quadratic+cubic effects together: i will have to use mri_glmfit with FSGD file. Best wishes Daniel... ___ 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] Rv: Fwd: Re: LME Guide + Developer Build
Hi Vivian The error you are getting means that the number of elements of your contrast vector is not the same as the number of columns of your design matrix. I think you're trying to apply the contrast matrix shown in the wiki page example to the sample dataset that we distribute with lme. That is incorrect. Note that the example in the wiki has four groups while the sample dataset only contains the data for two groups. Best -Jorge - Mensaje reenviado - De: Jorge jber...@nmr.mgh.harvard.edu Para: jbernal0...@yahoo.es Enviado: Domingo 29 de septiembre de 2013 23:24 Asunto: Fwd: Re: LME Guide + Developer Build Original Message Subject: Re: LME Guide + Developer Build Date: Sun, 29 Sep 2013 17:55:24 +0200 From: Vivian R. Steiger vivianroger.stei...@uzh.ch To: Jorge jber...@nmr.mgh.harvard.edu Hi Jorge I think its not a programming bug itself but an error in the text of the mass univariat example on the website: http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels Perfoming all steps until doing fine but: CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)]; F_lhstats = lme_mass_F(lhstats,CM); generates the following error in matlab: Error using lme_mass_F (line 49) The number of colums in the contrast matrix CM(1).C is different from the corresponding number of fixed effects in stats(1).Bhat Cheers Vivian Am 26.09.2013 um 16:58 schrieb Jorge jber...@nmr.mgh.harvard.edu: Yes, please send your questions to the Freesurfer's mailing list. Why do you think there is a bug in the inference step? Could you please send me the prompted error that you are getting and a snapshot of the cmd you typed and of the result of “whos” Matlab cmd? To test an omnibus F-contrast containing several rows you simply create the contrast matrix CM.C with one row for each individual contrast and then pass it on to lme_mass_F, eg. F_lhstats = lme_mass_F(lhstats,CM); Unlike the univariate setting, in the mass-univariate setting a structure array CM is passed on to the inference function instead of a plain matrix C because someone might be interested in using different contrasts across different vertices like CM(1).C, CM(2).C, ...(though unusual). If you are using the same contrast across vertices then you simply define CM.C and it will be used for all vertices. Eg. CM.C = [0 0 0 0 1 0 0 0; 0 0 0 0 0 0 0 1] for an F-test and CM.C = [0 0 0 0 1 0 0 0] for a T-test Best -Jorge On 09/26/2013 08:06 AM, Vivian R. Steiger wrote: Hi Jorge First of all thank you for your detailed response. We appreciate that you took time to answer us back. We've already done the tutorial with the ADNI dataset provided on the website, which worked quite well except of the part with CM.C where we think could be a bug. We eager to learn and process the lme for our structural dataset not just the t1-based but the dti as well and therefore we are interested in any new modelling toolboxes and paper dealing with lme survival analysis. We would be more than happy to beta-test such upcoming tools. The problem that we have right now is the adaptational steps from the tutorial to our own dataset and structure. Should we post such questions in the mailinglist or could we might ask you for some support? Normally a more direct path of q+a provides a better, faster and even more successful way to a solution :) Thank you for our time Best, Vivian 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 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.
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
___
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
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.
