On 05/07/2013 05:21 AM, Tudor Popescu wrote:

Hi Doug, I was just wondering whether you received my last email, with follow-ups on your answers. Sorry for the multitude of questions - as ever, I really appreciate the help! Best wishes, Tudor

On 4 May 2013 20:31, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:

Sorry Doug, wasn't sure whether you'd seen my reply
Tudor


---------- Forwarded message ----------
From: *Tudor Popescu* <tudor3@gmail.com <mailto:tudor3@gmail.com>>
Date: 2 May 2013 21:54
Subject: Re: [Freesurfer] ROI analyses
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>


Thanks Doug! If I may follow up:

    > 3) (I can't see whether there's a tutorial for this, as the
    main FS
    > site seems to be down at the moment) How can a group
    comparison of CT
    > be done inside a given ROI, and in what ways can the ROI be
    specified?
    > I guess the command line version of QDEC would produce, in
    this case,
    > the same contrasts as QDEC, but within the ROI as opposed to
    the whole
    > brain
    You mean you want to do an exploratory analysis within a mask
    of an ROI
    or that you want to average the CT scan within the ROI and do
    a group
    analysis of the ROI values? If the former, you can use
    mri_glmfit with
    the -label or -mask option. If the latter, you can create a
    table with
    asegstats2table then run mri_glmfit with --table

3') Is it the case that mri_glmfit with mask=brainmask.mgz is
equivalent to doing a whole-brain analysis in QDEC?

QDEC is only doing surface-based analysis. brainmask.mgz is a volume. But in principle the idea is similar.

3'')  I didn't find, on the mri_glmfit help page, how masks can be
formed out of one of the atlas structures, e.g.
"lh_S_intrapariet_and_P_trans "... The --table argument is also
not present anywhere on that page..

You can run mri_annotation2label to convert an annotation to label, then pass the label to glmfit.

3''') Would it not be a/parc/stats2table rather than
a/seg/stats2table, if the ROI in question was cortical and not
subcortical? Is the difference between what FS calls
"segmentation" and "parcellation" just terminology, i.e. the
former delineates subcortical structures and the latter delineates
cortical structures? Or does it imply anything else?

Whether you use one or the other depends on whether you generate the individual table with mris_anatomical_stats (aparcstats2table) or mri_segstats (asegstats2table)

    > 4) How do the results of these two different types of ROI group
    > analyses differ, and is one of them more "correct" than the
    other:
    >     A) running the command prompt version of QDEC within the
    confines
    > of a certain atlas-defined ROI, and looking at the resulting
    > statistical map (clusters), as per question 3;
    >     B) extracting the CT values for that ROI for all
    subjects using
    > aparcstats2table, and doing t-tests to look for a group
    difference.
    Oops, looks like these are the two I mentioned from #3 above.
    The first
    is an exploratory analysis in which the groups are compared on a
    vertex-by-vertex basis. If there is a subset of vertices that are
    different between the groups, it may show up in the exploratory
    analysis. However, the effect may be small at each vertex and
    averaging
    over the vertices may improve your power (unless the effect is
    only at a
    few vertices). One is not more correct than the other, just
    testing
    different hypotheses.

4') Can the second option (averaging the CT values within the ROI)
not also be done by taking the values from the table into SPSS and
simply doing an independent samples t-test? Is that not equivalent
to what mri_glmfit would do in this case?

Yes, it should be the same.

And one more question:
5) Can the statistical map in QDEC be built using a lower,
uncorrected p value (e.g. 0.0001) instead of an FDR-corrected test
value?

Yes, just set the threshold (FDR is off by default). doug

Thanks!!
Tudor

    doug

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    Douglas N. Greve, Ph.D.
    MGH-NMR Center
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