New subject: questions about cortical thickness using qdec.

9 Jan 2014

      Please remember to post to the list. For the 0 0 1 -1 contrast, did any 
results survive multiple comparisons correction? If so, then at least 
the voxels in that region cannot be used with DOSS. I'm not sure why the 
patter was opposite between the two contrasts. I could mean that there 
is a nonlinear relationship with age.
doug
On 01/09/2014 03:54 AM, yaya ya wrote:
...
Dear Greve,
Thank you very much for your response. I am now a little more clear, 
although I still have some further questions.
According to your suggestion, I just tried to test whether there is a 
difference between group age. I included age as a continuous variable 
in qdec. After running, I got the results arising from the contrast 0 
0 1 -1 (which is called does the thickness-age correlation differ 
between two groups?). That is, the results revealed the thinner in 
some brain areas. But when I checked the results relating to the 
comparision of groups (1 -1 0 0 ), the results were the same expect 
the opposite pattern. That is, the results became thicker in the same 
region.
Does this imply that there is an age effect? It means I could not use 
DOSS to do analysis, right?
Best,
Lickey
On Thu, Jan 9, 2014 at 12:32 AM, Douglas N Greve 
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 01/08/2014 04:28 PM, yaya ya wrote:
> Dear Freesurfer experts,
>
> I have a question about cortical thickness analysis using
freesurfer.
> Since I don't know how to post my question in freesurfer mailing
> list,  that is why I am writing to you to get some help.
Hopefully, my
> email will not cause you any troubles.
Thanks for posting to the list.
>
> My question is : When I compared thickness from two groups (a
patient
> group and a healthy contrl group), that is say I got the thinner
in a
> subdivision of a particular brain region in patients than that in
> controls. But when I added age as a nusiance factors (not in the
> continuous covariate because I want to control for or regress
out the
> age effect) in qdec, the results changed. In the same region,  the
> thickness became thicker in the patients than that in the
controls.  I
> have no idea what happened. Which of them do I need to trust?
The age
> between two groups has been matched.
It depends on several things. It might be that there is an interaction
between group and age. Try testing for a difference between the age
slopes of the two groups. If there is no difference, then re-run using
DOSS (DOSS was removed from QDEC so you'll have to create an FSGD file
and use mri_glmfit).
>
> In addition, when I do FDR correction on the results, the min in the
> threshold jumped to more than 5 , making all the clusters
disappear. I
> think this correction is too high, unabling the genious effects to
> show up. How to deal with it?
Try using a cluster correction instead of FDR.
doug

>
> By the way, our lab's IT staffs install the lastest released
> freesurfer. But when I use the qdec, I could not find the option of
> DODS and DOSS, as discussed in the mailing list. I am wondering
if it
> has been deleted in this new version.
>
> I really appreciate your help in advance.
>
> Best,
> Lickey
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Re: [Freesurfer] questions about cortical thickness using qdec.