Dear friends,
I am following this procedures to plot a 3D rendering of the AAL volume (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html).
My problem is the following. When I execute this command:
mri_cor2label --i lh.Colin27_aal2std.mgh --id 75 --l lh_Pallidum_L
specifically for the ROI Pallidum, a subcortical ROI, I receive the following error
$Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri lh.Colin27_aal2std.mgh Loading /Applications/freesurfer/subjects/FS_spm_CanonicalBrain/surf/lh.white Scanning the volume Found 0 label voxels ERROR: found no voxels matching id 75
This happens both for Pallidum Left and Pallidum Right, but all other AAL ROI work fine. I have an almost complete 3D rendering for my AAL. Only these subcortical regions are missing.
Someone knows what could be happening?
Thanks for the help.
best,
-- João V. Dornas Phd student in Neuroscience Cognitive Biology Group, Institute of Biology Otto von Guericke University, Magdeburg Germany
Did you check the volume to verify that at least one voxel has an index = 75 ?
On 3/19/16 10:43 AM, João V. Dornas wrote:
Dear friends,
I am following this procedures to plot a 3D rendering of the AAL volume (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html).
My problem is the following. When I execute this command:
*mri_cor2label --i lh.Colin27_aal2std.mgh --id 75 --l lh_Pallidum_L*
specifically for the ROI Pallidum, a subcortical ROI, I receive the following error
/$Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $/
/Loading mri lh.Colin27_aal2std.mgh/
/Loading /Applications/freesurfer/subjects/FS_spm_CanonicalBrain/surf/lh.white/
/Scanning the volume/
/Found 0 label voxels/
/ERROR: found no voxels matching id 75 /
This happens both for Pallidum Left and Pallidum Right, but all other AAL ROI work fine. I have an almost complete 3D rendering for my AAL. Only these subcortical regions are missing.
Someone knows what could be happening?
Thanks for the help.
best,
-- João V. Dornas Phd student in Neuroscience Cognitive Biology Group, Institute of Biology Otto von Guericke University, Magdeburg Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Freesurfer experts, I need some help with the longitudinal streaming and the use of mixed models in matlab. I followed all the instructions and tried to use the following commands in matlab:
lme_timePlot(M(:,1),Y,ni) and this worked well
However, when I tried this: lme_lowessPlot(M(:,1),Y,0.70,M(:,2))
matlab gave the following error message:
Undefined function 'smooth' for input arguments of type 'double'. Error in lme_lowessPlot (line 49) ybw = smooth(st,dat(ix),bw,'rlowess')
I checked in my version of matlab (R2012b) and the command 'smooth' does not exist
Further, when I tried this:
lhstats = lme_fit_FS(X,[1 2],Y,ni)
Error using - Matrix dimensions must agree.
Error in lme_fit_init (line 42) ri = yi-Xi*Bhat;
Error in lme_fit_FS (line 71) [D,phisq] = lme_fit_init(X,Zcols,y,ni);
Looking into the matlab code, I observed that in line 42 there is no command..... and I am sure that matrix dimensions are correct.
So, I have problems in solving these issues... Any help is greatly appreciated! Is it a problem of Matlab version? Thank you!
Angela
Hi Angela,
the smooth function seems to be part of the curve fitting toolbox http://www.mathworks.com/help/curvefit/smooth.html so either that is missing, or your version is too old. You can skip the lowess Plot (it is just for initially checking the data).
Make sure your M has the same number of rows as your Y (and as the sID). Also make sure you are computing the ni (and sorted M and Y) like this (if your first column in M is the time, else specify the column with the time as the second parameter):
[M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data)
Best, Martin
On 03/20/2016 04:38 PM, Angela Favaro wrote:
Dear Freesurfer experts, I need some help with the longitudinal streaming and the use of mixed models in matlab. I followed all the instructions and tried to use the following commands in matlab:
lme_timePlot(M(:,1),Y,ni) and this worked well
However, when I tried this: lme_lowessPlot(M(:,1),Y,0.70,M(:,2))
matlab gave the following error message:
Undefined function 'smooth' for input arguments of type 'double'. Error in lme_lowessPlot (line 49) ybw = smooth(st,dat(ix),bw,'rlowess')
I checked in my version of matlab (R2012b) and the command 'smooth' does not exist
Further, when I tried this:
lhstats = lme_fit_FS(X,[1 2],Y,ni)
Error using - Matrix dimensions must agree.
Error in lme_fit_init (line 42) ri = yi-Xi*Bhat;
Error in lme_fit_FS (line 71) [D,phisq] = lme_fit_init(X,Zcols,y,ni);
Looking into the matlab code, I observed that in line 42 there is no command..... and I am sure that matrix dimensions are correct.
So, I have problems in solving these issues... Any help is greatly appreciated! Is it a problem of Matlab version? Thank you!
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martin, thank you for your help. I still have problems in running mixed models analyses. Do I need some additional toolbox in matlab? (I did not find this information in the web) I tried to run the module in two versions of matlab, but the same problem occurr.
I used these commands: [M,Y,ni] = sortData(M,1,Y,sID) X = [ones(length(M),1) M M(:,1).*M(:,2)]
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3)
this is the error message: Undefined function 'matlabpool' for input arguments of type 'char'.
Error in lme_mass_fit_init (line 74) if (prs==1) || (matlabpool('size') ~= prs)
Error in lme_mass_fit_EMinit (line 69) [Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs);
What can it be the problem? the matrices seem to be OK (and M has the same number of rows as Y (and as the sID)).
thank you for any help!
Angela
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Hi Angela,
the smooth function seems to be part of the curve fitting toolbox http://www.mathworks.com/help/curvefit/smooth.html so either that is missing, or your version is too old. You can skip the lowess Plot (it is just for initially checking the data).
Make sure your M has the same number of rows as your Y (and as the sID). Also make sure you are computing the ni (and sorted M and Y) like this (if your first column in M is the time, else specify the column with the time as the second parameter):
[M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data)
Best, Martin
On 03/20/2016 04:38 PM, Angela Favaro wrote:
Dear Freesurfer experts, I need some help with the longitudinal streaming and the use of mixed models in matlab. I followed all the instructions and tried to use the following commands in matlab:
lme_timePlot(M(:,1),Y,ni) and this worked well
However, when I tried this: lme_lowessPlot(M(:,1),Y,0.70,M(:,2))
matlab gave the following error message:
Undefined function 'smooth' for input arguments of type 'double'. Error in lme_lowessPlot (line 49) ybw = smooth(st,dat(ix),bw,'rlowess')
I checked in my version of matlab (R2012b) and the command 'smooth' does not exist
Further, when I tried this:
lhstats = lme_fit_FS(X,[1 2],Y,ni)
Error using - Matrix dimensions must agree.
Error in lme_fit_init (line 42) ri = yi-Xi*Bhat;
Error in lme_fit_FS (line 71) [D,phisq] = lme_fit_init(X,Zcols,y,ni);
Looking into the matlab code, I observed that in line 42 there is no command..... and I am sure that matrix dimensions are correct.
So, I have problems in solving these issues... Any help is greatly appreciated! Is it a problem of Matlab version? Thank you!
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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.
Hi Angela,
newer versions of matlab don't support the old matlabpool comands any longer. You need to use an older matlab version (less than 8.2.0.29).
Best, Martin
On 04/05/2016 06:06 PM, Angela Favaro wrote:
Hi Martin, thank you for your help. I still have problems in running mixed models analyses. Do I need some additional toolbox in matlab? (I did not find this information in the web) I tried to run the module in two versions of matlab, but the same problem occurr.
I used these commands: [M,Y,ni] = sortData(M,1,Y,sID) X = [ones(length(M),1) M M(:,1).*M(:,2)]
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3)
this is the error message: Undefined function 'matlabpool' for input arguments of type 'char'.
Error in lme_mass_fit_init (line 74) if (prs==1) || (matlabpool('size') ~= prs)
Error in lme_mass_fit_EMinit (line 69) [Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs);
What can it be the problem? the matrices seem to be OK (and M has the same number of rows as Y (and as the sID)).
thank you for any help!
Angela
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Hi Angela,
the smooth function seems to be part of the curve fitting toolbox http://www.mathworks.com/help/curvefit/smooth.html so either that is missing, or your version is too old. You can skip the lowess Plot (it is just for initially checking the data).
Make sure your M has the same number of rows as your Y (and as the sID). Also make sure you are computing the ni (and sorted M and Y) like this (if your first column in M is the time, else specify the column with the time as the second parameter):
[M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data)
Best, Martin
On 03/20/2016 04:38 PM, Angela Favaro wrote:
Dear Freesurfer experts, I need some help with the longitudinal streaming and the use of mixed models in matlab. I followed all the instructions and tried to use the following commands in matlab:
lme_timePlot(M(:,1),Y,ni) and this worked well
However, when I tried this: lme_lowessPlot(M(:,1),Y,0.70,M(:,2))
matlab gave the following error message:
Undefined function 'smooth' for input arguments of type 'double'. Error in lme_lowessPlot (line 49) ybw = smooth(st,dat(ix),bw,'rlowess')
I checked in my version of matlab (R2012b) and the command 'smooth' does not exist
Further, when I tried this:
lhstats = lme_fit_FS(X,[1 2],Y,ni)
Error using - Matrix dimensions must agree.
Error in lme_fit_init (line 42) ri = yi-Xi*Bhat;
Error in lme_fit_FS (line 71) [D,phisq] = lme_fit_init(X,Zcols,y,ni);
Looking into the matlab code, I observed that in line 42 there is no command..... and I am sure that matrix dimensions are correct.
So, I have problems in solving these issues... Any help is greatly appreciated! Is it a problem of Matlab version? Thank you!
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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
Actually I am just adding a fix for this submitted by a user (thanks Knut) , so it should work with modern versions soon.
Best, Martin
On 04/06/2016 11:02 AM, Martin Reuter wrote:
Hi Angela,
newer versions of matlab don't support the old matlabpool comands any longer. You need to use an older matlab version (less than 8.2.0.29).
Best, Martin
On 04/05/2016 06:06 PM, Angela Favaro wrote:
Hi Martin, thank you for your help. I still have problems in running mixed models analyses. Do I need some additional toolbox in matlab? (I did not find this information in the web) I tried to run the module in two versions of matlab, but the same problem occurr.
I used these commands: [M,Y,ni] = sortData(M,1,Y,sID) X = [ones(length(M),1) M M(:,1).*M(:,2)]
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3)
this is the error message: Undefined function 'matlabpool' for input arguments of type 'char'.
Error in lme_mass_fit_init (line 74) if (prs==1) || (matlabpool('size') ~= prs)
Error in lme_mass_fit_EMinit (line 69) [Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs);
What can it be the problem? the matrices seem to be OK (and M has the same number of rows as Y (and as the sID)).
thank you for any help!
Angela
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Hi Angela,
the smooth function seems to be part of the curve fitting toolbox http://www.mathworks.com/help/curvefit/smooth.html so either that is missing, or your version is too old. You can skip the lowess Plot (it is just for initially checking the data).
Make sure your M has the same number of rows as your Y (and as the sID). Also make sure you are computing the ni (and sorted M and Y) like this (if your first column in M is the time, else specify the column with the time as the second parameter):
[M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data)
Best, Martin
On 03/20/2016 04:38 PM, Angela Favaro wrote:
Dear Freesurfer experts, I need some help with the longitudinal streaming and the use of mixed models in matlab. I followed all the instructions and tried to use the following commands in matlab:
lme_timePlot(M(:,1),Y,ni) and this worked well
However, when I tried this: lme_lowessPlot(M(:,1),Y,0.70,M(:,2))
matlab gave the following error message:
Undefined function 'smooth' for input arguments of type 'double'. Error in lme_lowessPlot (line 49) ybw = smooth(st,dat(ix),bw,'rlowess')
I checked in my version of matlab (R2012b) and the command 'smooth' does not exist
Further, when I tried this:
lhstats = lme_fit_FS(X,[1 2],Y,ni)
Error using - Matrix dimensions must agree.
Error in lme_fit_init (line 42) ri = yi-Xi*Bhat;
Error in lme_fit_FS (line 71) [D,phisq] = lme_fit_init(X,Zcols,y,ni);
Looking into the matlab code, I observed that in line 42 there is no command..... and I am sure that matrix dimensions are correct.
So, I have problems in solving these issues... Any help is greatly appreciated! Is it a problem of Matlab version? Thank you!
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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
I was finally able to run linear mixed models with my data - thank you very much Martin for your precious help!
No I would need some help/advice for visualization and description of my results
The command fs_write_Y(sided_pval,mri,'spval.mgh') is not working on my matlab. This is the message error: Error using reshape To RESHAPE the number of elements must not change. Error in fs_write_Y (line 21) save_mgh(reshape(Y',mri.volsz),fname,mri.M,mri.mr_parms);
so, I have used the command: fs_write_fstats(F_rhstats_lin,mri,'sig.mgh','sig') to export the findings, as described in the wiki. However, how can I describe my data, in terms of measure of the clusters, MNI coordinates and statistical values? and is it possible to smooth the image?
In addition, this map is 'uncorrected' for multiple testing. How can I perform this correction?
I am testing null hypothesis of no group differences in the rate of change over time between two groups and I found significant differences both using quadratic effects (time per time per group) and linear effects (time per group) in the same model (with one random effect, that appeared to perform better than the model with 2 RF). The map of the first analysis appeared in blue in Freeview, whereas the map for linear effects appeared in red. Does sig.mgh include the sign of the difference? and is it possible that the two analyses have opposite sign? am I doing something wrong?
Thank you!
Angela
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Actually I am just adding a fix for this submitted by a user (thanks Knut) , so it should work with modern versions soon.
Best, Martin
On 04/06/2016 11:02 AM, Martin Reuter wrote:
Hi Angela,
newer versions of matlab don't support the old matlabpool comands any longer. You need to use an older matlab version (less than 8.2.0.29).
Best, Martin
On 04/05/2016 06:06 PM, Angela Favaro wrote:
Hi Martin, thank you for your help. I still have problems in running mixed models analyses. Do I need some additional toolbox in matlab? (I did not find this information in the web) I tried to run the module in two versions of matlab, but the same problem occurr.
I used these commands: [M,Y,ni] = sortData(M,1,Y,sID) X = [ones(length(M),1) M M(:,1).*M(:,2)]
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3)
this is the error message: Undefined function 'matlabpool' for input arguments of type 'char'.
Error in lme_mass_fit_init (line 74) if (prs==1) || (matlabpool('size') ~= prs)
Error in lme_mass_fit_EMinit (line 69) [Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs);
What can it be the problem? the matrices seem to be OK (and M has the same number of rows as Y (and as the sID)).
thank you for any help!
Angela
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Hi Angela,
the smooth function seems to be part of the curve fitting toolbox http://www.mathworks.com/help/curvefit/smooth.html so either that is missing, or your version is too old. You can skip the lowess Plot (it is just for initially checking the data).
Make sure your M has the same number of rows as your Y (and as the sID). Also make sure you are computing the ni (and sorted M and Y) like this (if your first column in M is the time, else specify the column with the time as the second parameter):
[M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data)
Best, Martin
On 03/20/2016 04:38 PM, Angela Favaro wrote:
Dear Freesurfer experts, I need some help with the longitudinal streaming and the use of mixed models in matlab. I followed all the instructions and tried to use the following commands in matlab:
lme_timePlot(M(:,1),Y,ni) and this worked well
However, when I tried this: lme_lowessPlot(M(:,1),Y,0.70,M(:,2))
matlab gave the following error message:
Undefined function 'smooth' for input arguments of type 'double'. Error in lme_lowessPlot (line 49) ybw = smooth(st,dat(ix),bw,'rlowess')
I checked in my version of matlab (R2012b) and the command 'smooth' does not exist
Further, when I tried this:
lhstats = lme_fit_FS(X,[1 2],Y,ni)
Error using - Matrix dimensions must agree.
Error in lme_fit_init (line 42) ri = yi-Xi*Bhat;
Error in lme_fit_FS (line 71) [D,phisq] = lme_fit_init(X,Zcols,y,ni);
Looking into the matlab code, I observed that in line 42 there is no command..... and I am sure that matrix dimensions are correct.
So, I have problems in solving these issues... Any help is greatly appreciated! Is it a problem of Matlab version? Thank you!
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Angela,
to get the fs_write_Y to work, you would first need to set mri.volsz(4) = 1 (to tell it to write only a single frame).
But for writing significance maps, you can use fs_write_fstats (as you did).
Usually you don't describe the data, but simply capture the overlay of the p values on the surface and show the images. In the text you can of course reference the cortical ROI. You usually don't smooth significance maps, but instead you can use a different smoothing level for the inputs (Y, thickness), which is different.
For correction you would compute the FDR and use the result as a cutoff (FDR thresholded , so only what survives at the specified level is shown). Here it makes sense to combine left and right hemisphere. Something like this:
% FDR correct, then use - log10(pth) in tksurfer P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ]; [detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0); pcor = -log10(pth)
The significance map does include a sign, so that you know in what direction the effect goes. Having opposite signs for linear and quadratic is possible (meaning that the quadratic term goes in the opposite direction as the linear term). For example there could be a linear effect with age (atrophy, linear term is negative= higher age with smaller thickness) that slows down at higher ages (quadratic term is positive, a floor effect).
Best, Martin
On 04/20/2016 04:50 PM, Angela Favaro wrote:
I was finally able to run linear mixed models with my data - thank you very much Martin for your precious help!
No I would need some help/advice for visualization and description of my results
The command fs_write_Y(sided_pval,mri,'spval.mgh') is not working on my matlab. This is the message error: Error using reshape To RESHAPE the number of elements must not change. Error in fs_write_Y (line 21) save_mgh(reshape(Y',mri.volsz),fname,mri.M,mri.mr_parms);
so, I have used the command: fs_write_fstats(F_rhstats_lin,mri,'sig.mgh','sig') to export the findings, as described in the wiki. However, how can I describe my data, in terms of measure of the clusters, MNI coordinates and statistical values? and is it possible to smooth the image?
In addition, this map is 'uncorrected' for multiple testing. How can I perform this correction?
I am testing null hypothesis of no group differences in the rate of change over time between two groups and I found significant differences both using quadratic effects (time per time per group) and linear effects (time per group) in the same model (with one random effect, that appeared to perform better than the model with 2 RF). The map of the first analysis appeared in blue in Freeview, whereas the map for linear effects appeared in red. Does sig.mgh include the sign of the difference? and is it possible that the two analyses have opposite sign? am I doing something wrong?
Thank you!
Angela
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Actually I am just adding a fix for this submitted by a user (thanks Knut) , so it should work with modern versions soon.
Best, Martin
On 04/06/2016 11:02 AM, Martin Reuter wrote:
Hi Angela,
newer versions of matlab don't support the old matlabpool comands any longer. You need to use an older matlab version (less than 8.2.0.29).
Best, Martin
On 04/05/2016 06:06 PM, Angela Favaro wrote:
Hi Martin, thank you for your help. I still have problems in running mixed models analyses. Do I need some additional toolbox in matlab? (I did not find this information in the web) I tried to run the module in two versions of matlab, but the same problem occurr.
I used these commands: [M,Y,ni] = sortData(M,1,Y,sID) X = [ones(length(M),1) M M(:,1).*M(:,2)]
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3)
this is the error message: Undefined function 'matlabpool' for input arguments of type 'char'.
Error in lme_mass_fit_init (line 74) if (prs==1) || (matlabpool('size') ~= prs)
Error in lme_mass_fit_EMinit (line 69) [Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs);
What can it be the problem? the matrices seem to be OK (and M has the same number of rows as Y (and as the sID)).
thank you for any help!
Angela
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Hi Angela,
the smooth function seems to be part of the curve fitting toolbox http://www.mathworks.com/help/curvefit/smooth.html so either that is missing, or your version is too old. You can skip the lowess Plot (it is just for initially checking the data).
Make sure your M has the same number of rows as your Y (and as the sID). Also make sure you are computing the ni (and sorted M and Y) like this (if your first column in M is the time, else specify the column with the time as the second parameter):
[M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data)
Best, Martin
On 03/20/2016 04:38 PM, Angela Favaro wrote:
Dear Freesurfer experts, I need some help with the longitudinal streaming and the use of mixed models in matlab. I followed all the instructions and tried to use the following commands in matlab:
lme_timePlot(M(:,1),Y,ni) and this worked well
However, when I tried this: lme_lowessPlot(M(:,1),Y,0.70,M(:,2))
matlab gave the following error message:
Undefined function 'smooth' for input arguments of type 'double'. Error in lme_lowessPlot (line 49) ybw = smooth(st,dat(ix),bw,'rlowess')
I checked in my version of matlab (R2012b) and the command 'smooth' does not exist
Further, when I tried this:
lhstats = lme_fit_FS(X,[1 2],Y,ni)
Error using - Matrix dimensions must agree.
Error in lme_fit_init (line 42) ri = yi-Xi*Bhat;
Error in lme_fit_FS (line 71) [D,phisq] = lme_fit_init(X,Zcols,y,ni);
Looking into the matlab code, I observed that in line 42 there is no command..... and I am sure that matrix dimensions are correct.
So, I have problems in solving these issues... Any help is greatly appreciated! Is it a problem of Matlab version? Thank you!
Angela
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-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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thank you!
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Hi Angela,
to get the fs_write_Y to work, you would first need to set mri.volsz(4) = 1 (to tell it to write only a single frame).
But for writing significance maps, you can use fs_write_fstats (as you did).
Usually you don't describe the data, but simply capture the overlay of the p values on the surface and show the images. In the text you can of course reference the cortical ROI. You usually don't smooth significance maps, but instead you can use a different smoothing level for the inputs (Y, thickness), which is different.
For correction you would compute the FDR and use the result as a cutoff (FDR thresholded , so only what survives at the specified level is shown). Here it makes sense to combine left and right hemisphere. Something like this:
% FDR correct, then use - log10(pth) in tksurfer P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ]; [detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0); pcor = -log10(pth)
The significance map does include a sign, so that you know in what direction the effect goes. Having opposite signs for linear and quadratic is possible (meaning that the quadratic term goes in the opposite direction as the linear term). For example there could be a linear effect with age (atrophy, linear term is negative= higher age with smaller thickness) that slows down at higher ages (quadratic term is positive, a floor effect).
Best, Martin
On 04/20/2016 04:50 PM, Angela Favaro wrote:
I was finally able to run linear mixed models with my data - thank you very much Martin for your precious help!
No I would need some help/advice for visualization and description of my results
The command fs_write_Y(sided_pval,mri,'spval.mgh') is not working on my matlab. This is the message error: Error using reshape To RESHAPE the number of elements must not change. Error in fs_write_Y (line 21) save_mgh(reshape(Y',mri.volsz),fname,mri.M,mri.mr_parms);
so, I have used the command: fs_write_fstats(F_rhstats_lin,mri,'sig.mgh','sig') to export the findings, as described in the wiki. However, how can I describe my data, in terms of measure of the clusters, MNI coordinates and statistical values? and is it possible to smooth the image?
In addition, this map is 'uncorrected' for multiple testing. How can I perform this correction?
I am testing null hypothesis of no group differences in the rate of change over time between two groups and I found significant differences both using quadratic effects (time per time per group) and linear effects (time per group) in the same model (with one random effect, that appeared to perform better than the model with 2 RF). The map of the first analysis appeared in blue in Freeview, whereas the map for linear effects appeared in red. Does sig.mgh include the sign of the difference? and is it possible that the two analyses have opposite sign? am I doing something wrong?
Thank you!
Angela
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Actually I am just adding a fix for this submitted by a user (thanks Knut) , so it should work with modern versions soon.
Best, Martin
On 04/06/2016 11:02 AM, Martin Reuter wrote:
Hi Angela,
newer versions of matlab don't support the old matlabpool comands any longer. You need to use an older matlab version (less than 8.2.0.29).
Best, Martin
On 04/05/2016 06:06 PM, Angela Favaro wrote:
Hi Martin, thank you for your help. I still have problems in running mixed models analyses. Do I need some additional toolbox in matlab? (I did not find this information in the web) I tried to run the module in two versions of matlab, but the same problem occurr.
I used these commands: [M,Y,ni] = sortData(M,1,Y,sID) X = [ones(length(M),1) M M(:,1).*M(:,2)]
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3)
this is the error message: Undefined function 'matlabpool' for input arguments of type 'char'.
Error in lme_mass_fit_init (line 74) if (prs==1) || (matlabpool('size') ~= prs)
Error in lme_mass_fit_EMinit (line 69) [Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs);
What can it be the problem? the matrices seem to be OK (and M has the same number of rows as Y (and as the sID)).
thank you for any help!
Angela
Martin Reuter mreuter@nmr.mgh.harvard.edu ha scritto:
Hi Angela,
the smooth function seems to be part of the curve fitting toolbox http://www.mathworks.com/help/curvefit/smooth.html so either that is missing, or your version is too old. You can skip the lowess Plot (it is just for initially checking the data).
Make sure your M has the same number of rows as your Y (and as the sID). Also make sure you are computing the ni (and sorted M and Y) like this (if your first column in M is the time, else specify the column with the time as the second parameter):
[M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data)
Best, Martin
On 03/20/2016 04:38 PM, Angela Favaro wrote: > Dear Freesurfer experts, > I need some help with the longitudinal streaming and the use of mixed > models in matlab. > I followed all the instructions and tried to use the following > commands in matlab: > > lme_timePlot(M(:,1),Y,ni) > and this worked well > > However, when I tried this: > lme_lowessPlot(M(:,1),Y,0.70,M(:,2)) > > matlab gave the following error message: > > Undefined function 'smooth' for input arguments of type 'double'. > Error in lme_lowessPlot (line 49) > ybw = smooth(st,dat(ix),bw,'rlowess') > > I checked in my version of matlab (R2012b) and the command 'smooth' > does not exist > > Further, when I tried this: > > lhstats = lme_fit_FS(X,[1 2],Y,ni) > > Error using - > Matrix dimensions must agree. > > Error in lme_fit_init (line 42) > ri = yi-Xi*Bhat; > > Error in lme_fit_FS (line 71) > [D,phisq] = lme_fit_init(X,Zcols,y,ni); > > Looking into the matlab code, I observed that in line 42 there is no > command..... > and I am sure that matrix dimensions are correct. > > So, I have problems in solving these issues... Any help is greatly > appreciated! > Is it a problem of Matlab version? > Thank you! > > Angela > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
>
Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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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
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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