Yes, see the answer to your first question below. doug krista kelly wrote: > Am I able to do vertex-by-vertex analyses using freesurfer if I have > more than 2 discrete variables? If so, how? > > Is it also ok to use the unsmoothed data when doing surface area label > analyses? > > Thanks! > > On Tue, Oct 18, 2011 at 3:14 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Sorry, I meant to say that you cannot use QDEC with more than 2 > discrete variables (you have 3). You do not need to extract data > from the smoothed thickness files, but the results you get from > your ROI analysis may then differ a bit from that you get from the > QDEC analysis. > doug > > krista kelly wrote: > > Thanks Doug! Just a few more things: > > I only have two groups, so my contrast was wrong. Should it > only be 1 -1, even if I have other variables I want to control > for? Or should I have a contrast file for each discrete variable? > > How would I extract the smoothed data using mri_anatomical_stats? > > I realize the importance of smoothing data while doing a > vertex-by-vertex analysis in QDec, but if I'm doing an ROI > analysis by extracting the average thickness in a certain > label (i.e. v1), is it necessary to do the stats on the > smoothed data from each participant? > > Thanks! > > > On Tue, Oct 18, 2011 at 2:23 PM, 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: > > > > krista kelly wrote: > > Hi, just wondering if anyone has any advice on the > following > questions: > > I'm using QDEC to analyze cortical thickness differences > between groups and I have a few questions: > > 1) There are a few variables that I need to control > for. First > variable is scanner - I used two different scanners of > different field strengths (1.5T GE and 3T Siemens) so I > wanted > to control for scanner. I also wanted to control for > age and > gender. Here's my ideal design setup: > > discrete variables - groups, scanner, gender > nuisance variable - age > > contrast would be 1 -1 0 0 0 0 > I realize that scanner, gender, and group are all discrete > variables, and that age would be a continuous one. > However, in > the design tab, I am not able to select all 3 discrete > variables (groups, scanner, and gender). Should I designate > scanner or gender as a nuisance variable instead? Would it > matter which one I use as the nuisance variable? > Possible setup: > > discrete vars - groups, scanner > nuisance vars - age, gender > > contrast - 1 -1 0 0 (Correct?) > > Unfortunately, you cannot use QDEC if you have three groups. > You'll have to create an FSGD file and contrasts by hand, > then run > mri_glmfit. Do a search for FSGD on our wiki and go to the > examples page. I think there is an example there for what > you want > to do. > > > 2) If I use DODS, should I demean the ages if age is a > nuisance variable? > > You should actually test whether there is an interaction > between > age and your group contrast of interest (using the DODS > model). If > there is not interaction, then switch to a DOSS where demeaning > does not matter. > > > 3) If I use a smoothing kernel during the analysis, then > create an ROI and map that ROI to each individual subject, > will the resulting .stats file in each subjects stats > folder > reflect the smoothed data or does mapping onto each ROI > just > extract the raw unsmoothed data from each vertex? > > It depends on how you do the extraction. If you are using > mris_anatomical_stats on each individual's unsmoothed data, > then > it will reflect the unsmoothed. > > doug > > > Thanks! > Krista > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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: > 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> > > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
