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can you send the cluster summary file?

On 11/24/2019 7:09 PM, Bronwyn Overs wrote:

        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). 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

neura.edu.au 

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From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, "Kersten Diers, DZNE" <Kersten.Diers@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
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>
>
>
>
> ------------------------------------------------------------------------
> *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
>
> 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>
>
>
>
>
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