Hi Douglas,
Yes I have looked at it in Freeview and I have attached a screenshot for your reference.
The /fsdata/lme/thickness/rh.thickness.B1B7.mgh file was generated with a mass-univariate spatiotemporal model using 'lme_mass_fit_EMinit' and then FDR correction was applied across both hemispheres (lme_mass_FDR). I have provided analysis details and syntax below. The B1B7 contrast represents the affect of years in cases.
Sample:
Our sample includes 112 controls subjects, and 106 cases. All subjects are aged between 12 and 30 years. 153 or these subjects have 2 time-points (77 control, 76 cases), while the remaining 65 individuals have only 1 MRI time-point. We also have mixed ethnicites - 165 Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians).
The QDEC file contains the following 6 variables:
1. Y (years between scans)
2. A (baseline age)
3. G (group, 1=case, 0=control)
4. S (sex, 1=female, 0=male)
5. E1 (Ethnicity 1, 1=asian, 0=other)
6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other)
Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)]
i.e. main effects for each of the qdec variables + an interaction term for years X group
DVs: Cortical thickness, area and volume
Model: Mass-univariate spatiotemporal model using
'lme_mass_fit_EMinit'
CODE:
% Read in surface files
[Y,mri] = fs_read_Y(mgh);
% Read in qdec file
Qdec = fReadQdec(qdec);
% Remove fsid from qdec
Qdec = rmQdecCol(Qdec,1);
% Store col 1 (fsid-base) in sID variable
sID = Qdec(2:end,1);
% Remove col 1 (fsid-base) from Qdec array
Qdec = rmQdecCol(Qdec,1);
% Convert Qdec to numeric matrix M
M = Qdec2num(Qdec);
% Sort data and evaluate design matrix
[M,Y,ni] = sortData(M,1,Y,sID);
X = eval([ones(length(M),1) M M(:,1).*M(:,3)])
% Compute vertex-wise temporal covariance estimates.
[Th0, Re] = lme_mass_fit_EMinit(X,[1],Y,ni,cortex,3);
%Segmentation and model fitting.
[Rgs, RgMeans, stats] = fit(Th0, Re, [1], sphere, cortex, X, Y,
ni);
%Check surfaces.
surfcomp(Th0, RgMeans, sphere, fig1, fig2)
Correction for multiple comparisons: FDR across both hemispheres
CODE:
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);
altfdr(r,2) = num2cell(abs(log10(lme_mass_FDR(P,0.05))));
pcor = -log10(pth);
[~,~,dflh] = find(F_lhstats.df(2,:));
[~,~,dfrh] = find(F_rhstats.df(2,:));
dfmodelh(r,2) = {floor(mode(dflh))};
dfmoderh(r,2) = {floor(mode(dfrh))};
thrlh(r,2) = {pcor};
thrrh(r,2) = {pcor};
[~,dc] = size(detvtx);
dvtx(r,2) = {dc};
Our sample includes 112 controls subjects, and 106 cases. All subjects are aged between 12 and 30 years. 153 or these subjects have 2 time-points (77 control, 76 cases), while the remaining 65 individuals have only 1 MRI time-point. We also have mixed ethnicites - 165 Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians).
The QDEC file contains the following 6 variables:
1. Y (years between scans)
2. A (baseline age)
3. G (group, 1=case, 0=control)
4. S (sex, 1=female, 0=male)
5. E1 (Ethnicity 1, 1=asian, 0=other)
6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other)
Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)]
i.e. main effects for each of the qdec variables + an interaction term for years X group
DVs: Cortical thickness, area and volume
Model: Mass-univariate spatiotemporal model using
'lme_mass_fit_EMinit'
CODE:
% Read in surface files
[Y,mri] = fs_read_Y(mgh);
% Read in qdec file
Qdec = fReadQdec(qdec);
% Remove fsid from qdec
Qdec = rmQdecCol(Qdec,1);
% Store col 1 (fsid-base) in sID variable
sID = Qdec(2:end,1);
% Remove col 1 (fsid-base) from Qdec array
Qdec = rmQdecCol(Qdec,1);
% Convert Qdec to numeric matrix M
M = Qdec2num(Qdec);
% Sort data and evaluate design matrix
[M,Y,ni] = sortData(M,1,Y,sID);
X = eval([ones(length(M),1) M M(:,1).*M(:,3)])
% Compute vertex-wise temporal covariance estimates.
[Th0, Re] = lme_mass_fit_EMinit(X,[1],Y,ni,cortex,3);
%Segmentation and model fitting.
[Rgs, RgMeans, stats] = fit(Th0, Re, [1], sphere, cortex, X, Y,
ni);
%Check surfaces.
surfcomp(Th0, RgMeans, sphere, fig1, fig2)
Correction for multiple comparisons: FDR across both hemispheres
CODE:
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);
altfdr(r,2) = num2cell(abs(log10(lme_mass_FDR(P,0.05))));
pcor = -log10(pth);
[~,~,dflh] = find(F_lhstats.df(2,:));
[~,~,dfrh] = find(F_rhstats.df(2,:));
dfmodelh(r,2) = {floor(mode(dflh))};
dfmoderh(r,2) = {floor(mode(dfrh))};
thrlh(r,2) = {pcor};
thrrh(r,2) = {pcor};
[~,dc] = size(detvtx);
dvtx(r,2) = {dc};
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, November 13, 2019 2:44:25 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, November 13, 2019 2:44:25 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file
It looks like you have one gigantic cluster with a value of -inf at vertex 41. How did you generate /fsdata/lme/thickness/rh.thickness.B1B7.mgh ? Have you looked at it in freeview?
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On 11/11/2019 7:39 PM, Bronwyn Overs wrote:
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Dear Freesurfer Mailing List,
I have completed an LME analysis in matlab and have generated a number of different cluster summary files for my various contrasts. In many of resulting cluster summary files the 'Max' value for the largest cluster which encompasses most of the brain surface is reported as infinity ('-inf'). Please find an example file attached. As I was hoping to use these values to generate effect size estimates, can you please tell me what alternate value I could substitute here for 'Max'?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer@nmr.mgh.harvard.edu
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