External Email - Use Caution Hi Kersten,
Following on from Douglas's reply, you may remember my analysis as I forwarded you some files in October (see [ https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html | https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html ] ). I followed your suggestions of removing the '--thmax 5' argument form 'mri_surfcluster', and now the labels generated by 'mri_label2label' overlap perfectly with the significance maps from the LME. However, now my largest clusters have a maximum threshold of '-inf' in my cluster summary files. Do you have any idea how to get around this problem so that I can use my max threshold values to calculate cluster-wise effect sizes? 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 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, "Kersten Diers, DZNE" <kersten.di...@dzne.de> Sent: Thursday, November 14, 2019 4:23:12 AM Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file I'll have to leave this one for Kersten as it appears that the LME stuff is generating and inf value On 11/12/19 7:05 PM, Bronwyn Overs wrote: > > External Email - Use Caution > > 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}; > > 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 > > > neura.edu.au <http://neura.edu.au/> > > Twitter <https://twitter.com/neuraustralia> | Facebook > <https://www.facebook.com/NeuroscienceResearchAustralia> | Subscribe > <http://www.neura.edu.au/help-research/subscribe> > > > > > ------------------------------------------------------------------------ > *From: *"Greve, Douglas N.,Ph.D." <dgr...@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 > > 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? > > On 11/11/2019 7:39 PM, Bronwyn Overs wrote: > > External Email - Use Caution > > 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 > > > neura.edu.au <http://neura.edu.au/> > > Twitter <https://twitter.com/neuraustralia> | Facebook > <https://www.facebook.com/NeuroscienceResearchAustralia> | > Subscribe <http://www.neura.edu.au/help-research/subscribe> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 > > _______________________________________________ > 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
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