thank you!
Martin Reuter <mreu...@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 <mreu...@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 <mreu...@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
>>>>>>
>>>>>>
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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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>>
>
> --
> 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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