Do you mean aseg.volume also contains the volume of cortical structures as well, not just subcortical? If so, how can one retrieve those?

> - how are the volume measurements provided in aseg.volume
> different from the ones done obtained with a VBM analysis?
>
Does VBM give segmentation volumes? I thought it was voxel-wise exploratory.

I was making a confusion here: in FSL, it's not FSL_VBM that gives you the volume of a given structure, but FSLSTATS, when used with a certain mask/ROI. My question is, then, whether the volume measurements provided in aseg.volume are similar to what you would get with FSLSTATS, with the exception that aseg.volume uses automatic segmentation rather than a cutom-defined mask

> - how is a QDEC thickness analysis different from a regular
> AN(C)OVA in which you are interested in main and interaction
> effects of the IVs on the DV? I ask this because some of the
> questions that appear in QDEC's Analysis Results tab – e.g. "is
> the correlation between (DV) and (IV) different from zero?" –
> would not (I think) be directly answerable by an ANOVA
>
Often times they are the same, depends on the contrast. I don't know
what IV and DV are so I can't answer your specific question.

IV = independent variable; DV = dependent variable.
Since in QDEC you can't define the contrast vector directly (it's created automatically, if I understand it correctly), then it seems to me that the analysis is just an AN(C)OVA, so I still don't understand how questions such as the one about the correlation being non-zero can be answered..

Thanks again very much Doug!!

On 28 March 2013 20:07, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

On 03/28/2013 03:53 PM, Tudor Popescu wrote:
> I was wondering if anybody is able to help with (any one of) these
> questions? That would be really helpful, as I could not find an answer
> on the wiki.
>
> Many thanks in advance!
>
> On 26 March 2013 20:44, Tudor Popescu <tudor3@gmail.com

> <mailto:tudor3@gmail.com>> wrote:
>
> Hi everyone,
>
>
> My QDEC analysis ran into an error message that seems to be a
> "classic" (and, so far, it seems unsolved), from mri_concat, which
> I've described in a separate message, just sent.
>
>
> I have, however, more theoretical questions about QDEC, which I
> hope some kind soul will help me with:
>
>

> - why does QDEC only provide the volume of /subcortical/

> structures under StatsDataImport/aseg.volume, when the automatic
> GM/WM segmentation is done for the entire brain, not just for
> subcortical regions?
>

No reason in particular. You can add them into the qdec table.

>
>
> - how are the volume measurements provided in aseg.volume
> different from the ones done obtained with a VBM analysis?
>

Does VBM give segmentation volumes? I thought it was voxel-wise exploratory.
>
> - why is /volume /the result of /segmentation /(aseg.volume)
> whereas /thickness /derives from /parcelation
> /(rh.aparc.thickness)? Is it not the case that both operations

> (segmentation+parcellation) are necessary to calculate volume as
> well as thickness?
>

You can get volume from parcellations too (this is supplied in the
?h.apac.stats file). You can't get thickness from non-surface structures
like amygdala.

>
>
> - how is a QDEC thickness analysis different from a regular
> AN(C)OVA in which you are interested in main and interaction
> effects of the IVs on the DV? I ask this because some of the
> questions that appear in QDEC's Analysis Results tab – e.g. "is
> the correlation between (DV) and (IV) different from zero?" –
> would not (I think) be directly answerable by an ANOVA
>

Often times they are the same, depends on the contrast. I don't know
what IV and DV are so I can't answer your specific question.

>
> - would the same type of ANOVA done by QDEC be doable by
> extracting the values of the DV for each subject (using e.g.

> /aseg.volume/) and then doing the ANOVA in e.g. SPSS? If so, when

> would you do one versus the other?
>

Yes. QDEC is an exploratory voxel-based method so effects don't have to
lie cleanly within an ROI boundary.

>
> - why is it that only continuous factors (e.g. age) can be taken
> in the analysis as nuisance factors, when discrete variables (e.g.
> gender) might also be irrelevant for a particular analysis and
> thus belong to the Nuisance Factor list?
>

It is just a matter of convenience in making the contrasts. ie, it is
easy to extend our contrast making code to add nuisance continuous variables
doug

>
> Many thanks in advance!!
>
> Tudor
>
>
>
>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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