Re: [Freesurfer] interpreting qdec results

If you go into the QDEC folder, you will see a file called Xg.dat, go into matlab and load this file

X = load('Xg.dat'); Set a variable called y to the list of thicknesses for the cluster with the subjects sorted in the same order as that find in y.fsgd beta = inv(X'*X)*X'*y beta will have as many entries as there are columns in X. From what you said about your design, this should be 4. The first will be the mean thickness for the controls regressing out age, the second for the patients, the 3rd will be the age slope for controls, the 4th will be the age slope for patients

doug

On 06/26/2014 08:09 AM, Emma Thompson wrote:

That would be especially helpful, thanks Doug. I have another related question. In addition to measuring cortical thickness, I've also done the same analysis using the cortical surface volume measure in Qdec. For this analysis I used age and mean centered total intercranial volume (TIV) as nuisance variables. After running the analysis, the graph is displayed showing the volume on the y axis and mean centered TIV on the y axis. When I extract the data I get volume values in the 2.0016 - 2.7268 range, I was expecting to see values on the order of 1500-1600 or so, is this because qdec is giving me cortical volume values that have been normalized to TIV?

Thanks again for all your help!

On Wed, Jun 25, 2014 at 5:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

No, I've never used SPSS. If you know matlab, I can step you
through how
to do it there

On 06/25/2014 04:13 PM, Emma Thompson wrote:
> I'm using SPSS. I'm not sure if my analysis reflects exactly
what qdec
> is doing, do you know which analysis in SPSS would be most
> appropriate? I'm doing a simple ANCOVA.
>
>
> On Wed, Jun 25, 2014 at 11:07 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>
>
>     what software did you use? Are you sure you are using the same
>     model as
>     qdec uses?
>
>
>     On 06/25/2014 11:03 AM, Emma Thompson wrote:
>     > Thanks Doug, yes I did control for age in both instances.
>     >
>     >
>     > On Wed, Jun 25, 2014 at 10:14 AM, Douglas N Greve
>     > <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
>     >
>     >
>     >     Your interpretation is right (ie, controls > patients for
>     >     red/yellow/orange). When you compared the two groups
in your
>     separate
>     >     analysis, did you control for age?
>     >     doug
>     >
>     >
>     >     On 06/24/2014 02:19 PM, Emma Thompson wrote:
>     >     > Hi Freesurfers,
>     >     > I am reposting this as my last email bounced.
>     >     >
>     >     > I have conducted a DODS analysis in qdec with group
>     (controls vs
>     >     > patients) set as my fixed factor and age as a nuisance
>     variable to
>     >     > determine if my groups differ in cortical thickness.
>     Controls were
>     >     > added first in the .levels file followed by
patients. When I
>     >     view the
>     >     > results in the display window for "do controls
differ from
>     >     patients in
>     >     > cortical thickness" I see a significant cluster for
the caudal
>     >     > anterior cingulate, denoted by a red-orange blob and a
>     positive
>     >     > t-value. I'm wondering if this simply means that
controls had
>     >     greater
>     >     > cortical thickness compared to patients after
controlling for
>     >     age? The
>     >     > reason I ask is that I'm a little confused since when I
>     created
>     >     an ROI
>     >     > for this cluster using tksurfer and then extracted the
>     means and
>     >     sd, I
>     >     > see that the patients actually have larger means
than the
>     controls,
>     >     > the opposite of my interpretation of the results
presented by
>     >     the qdec
>     >     > display. Furthermore, if I extract the means and sds for
>     the entire
>     >     > caudal anterior cingulate using the aparc file, I get
>     means that are
>     >     > larger in controls, compared to patients, which seems
>     consistent
>     >     with
>     >     > qdec. Any ideas? Thanks for all the help.
>     >     >
>     >     >
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