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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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> > <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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
