Is this an analysis of volume/voxel data or surface/vertex data? If
surface, then you'll need to extract the left insula label from
lh.aparc.annot (use mri_annotation2label), then pass this label to
mri_glmfit with --label
doug
On 01/09/2014 03:52 PM, yaya ya wrote:
> Thanks, Doug.
>
> I just searched the list to find how to generate a mask. Let us say
> the surface of the left insula.
>
> It seems that I need to use mri_mask command and the brain which I use
> to get the mask should be brainmask.mgz in the fsaverage, right?
>
> Then I use this mask in mri_glmfit command.
>
> Any suggstions, feel free to let me know.
>
>
> On Thu, Jan 9, 2014 at 9:13 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
> On 01/09/2014 02:18 PM, yaya ya wrote:
> > Dear Doug,
> >
> > I am sorry. It is my first time to post the message in this way.
> I am
> > now used to it:)
> >
> > The results from the contrast 0 0 1 -1 did not survive the multiple
> > comparision corrections. In other words, I guess that it should
> imply
> > that I could try DOSS.
> >
> > If my thought is wrong, please feel free to let me know.
> You are correct.
> >
> > By the way, is it possible to do SVC (small volume correction) using
> > an anatomical image from a particular brain region, which is the
> > conventional way to improve statistical power?
> You can specify a mask for an ROI when you run mri_glmfit. But that
> means you have to run your own simulation to do the correction.
> doug
>
>
> >
> > Thanks, again.
> >
> >
> > On Thu, Jan 9, 2014 at 6:23 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> >
> > 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>
> <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:
> >
> >
> > 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>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto: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>
> <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>>>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358>>
> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
> <tel:617-724-2358>>>
> > Fax: 617-726-7422 <tel:617-726-7422>
> <tel:617-726-7422>
> > <tel:617-726-7422 <tel:617-726-7422>>>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://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>
> >
> <http://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>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358>>
> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
> <tel:617-726-7422>>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://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>
> > <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
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> _______________________________________________
> 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
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/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer