Ty Doug,

Kind regards, 
Egil 
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve 
<gr...@nmr.mgh.harvard.edu>
Sent: 23 March 2015 17:45
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Question regarding Qdec vs mri_glmfit outputs

Use the result from mri_glmfit.
doug

On 03/20/2015 10:20 AM, Egil Nygaard wrote:
>
> Dear Freesurfer support,
>
> I find the qdec to be very pedagogic in its outlay, and would love to
> use it. However, I find several discrepancies as compared to results
> from the mri_glmfit analyses, and wonder why (see description below).
>
> 1) One discrepancy is the placement of the clusters; X, Y, Z's. Should
> I use:
>
>  *
>     the figures from the result summary from mri_glmfit,
>  *
>     the result summary from Qdec (which is almost the same as from the
>     results summary from mri_glmfit),
>  *
>     or from the “Find clusters and goto max” function in the display
>     window of Qdec (which shows very different placements than the two
>     others)?
>
> 2) Which size should I use? The sizes of the clusters from qdec are
> 1-2% smaller than what are reported from the mri_glmfit analyses.
>
> I expect that the reason for the discrepancies is that I probably do
> something different in the mri_glmfit analyses than the standard Qdec
> analyses, but I can not figure out what it is.
>
>
>
> Below is information about which analyses I have done and some more
> information about the Qdec output.
> **
>
> *Overview analyses:*
>
> We investigate difference between two groups. We have two sets of
> data, one with skewed age and gender distribution between groups (n =
> 89) (older participants and more girls in the risk group), and one
> with 33 extra control participants (n = 122) making the risk and
> control group having similar age and gender distribution.
>
> The vertex based analyses are done with mri_glmfit in Freesurfer
> version 5.3. I have analyzed the data both with DOSS and DODS. Both
> without covariates, controlling for age (demeaned continuous variable)
> or controlling for gender, or controlling for both age and gender. We
> have used smoothing fwhm 10. The results were controlled for multiple
> comparisons with the standard mri_glmfit-sim method in Freesurfer with
> cache 1.3 abs and 2spaces (did not use 2spaces when comparing
> mri_glmfit results with Qdec results).
>
> We have used tksurfer (DOSS and DODS) and qdec (DODS) to visualize the
> results, but mainly used results from
> cache.th13.abs.sig.cluster.summary files to compare with the analyses
> from SPSS.
>
> The contrast in the full DODS model in the mri_glmfit is 1 1 -1 -1 0 0
> 0 0, with the fsgd file being:
>
> GroupDescriptorFile 1
> Title n89-33
> Class group1risk_gender1girl
> Class group1risk_gender2boy
> Class group2control_gender1girl
> Class group2control_gender2boy
> Variables age
> Input UN001 group1control_gender2boy -1.0172131148
> Etc
>
> Preproc was done with:
>
> mris_preproc --target fsaverage --hemi lh --meas area --fsgd
> $glm/demographicn122.fsgd --out $preproc
>
> Smoothing was done with:
> mri_surf2surf --hemi lh --s fsaverage --sval $preproc --fwhm 10
> --cortex --tval $smoothing10
>
> GLM was done with:
>
> mri_glmfit --glmdir $contrast --y $smoothing10 --fsgd
> $glm/demographicn122.fsgd --C $glm$contrast_kjal.mat --surf fsaverage
> lh --cortex
>
> Correction for multiple comparisons was done with:
>
> mri_glmfit-sim --glmdir $contrast --cache 1.3 abs
>
> *Qdec:*
> There are discrepancies between results from qdec and mri_glmfit. I am
> unsure why. I notice for example that there are small discrepancies in
> the fwhm.dat files from Qdec and mri_glmfit. The most important for my
> use is that when I compare the clusters in the file:
> cache.th13.abs.sig.cluster.summary from the mri_glmfit, and the
> clusters from the file: mc-z.abs.th13.sig.cluster.summary from qdec, I
> find the same four clusters of group differences in cortex areas with
> the same Max number and Vtxmax. However, the sizes are marginally
> different, with the sizes from qdec being 1-2% smaller. Most
> importantly for me are the differences in the placement of the
> clusters. The MNIX, Y and Z from mri_glmfit are not similar to the
> TalX, Y and Z from Qdec. The differences are not big, but still
> significant for us. I also note that the TalX, Y and Z's from the
> result file from Qdec is very different from the  TalX, Y and Z's from
> the output one get from Qdec when one use the button “Find clusters
> and got max” in the visual Display window in Qdec. It seems the output
> from Qdec's “Find clusters and got max” shows the mean cluster
> placement (all Max figures are 4), whereas the output from mri_glmfit
> and from the resultsfile from Qdec shows the placement of masked
> clusters (the Max figures vary)?
>
> Kind regards,
>
> Egil Nygaard
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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