Antonella Kis wrote: > Hi Doug, > > 1) I would like to report the MNI coordinates and also a more exactly > region I mean if possible tto find exactly where in the > Left-Cerebral-White-Matter and Right-Cerebral-White-Matter my cluster > is located. What do you me by "exactly where"? The nearest cortical label? The fiber bundle? > > 2)Can you please tell me if for the mean diffusivity I should use the > simulation with the perm (as I use for the FA due to the fact that is > not so Gaussian) option or it is OK to use the grf option. I think you can use GRF for this as it corresponds to a normal contrast in a GLM. Note that the permutation is the stronger (but more conservative) test. > > > 3) Can you please explain what exactly means for my clusters if I hit > the positive sign under DISPLAY in Qdec? I mean if I compare the > cortical thickness between two classes: controls vs. Patients and > I am not interested in the sex or age differences just differences > between the two classes will positive mean clusters where cortical > thickness graeter in Class 1 than Class2 (Class1>Class2)? > > I have C = +1 -1 and my Class 1 = controls while Class2 = PAtients. Positive is Controls > Patients
doug > > > THANKS YOU. > Antonella > ------------------------------------------------------------------------ > *From:* Douglas Greve <gr...@nmr.mgh.harvard.edu> > *To:* Antonella Kis <ator...@yahoo.com>; free surfer > <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Tuesday, February 14, 2012 9:59 AM > *Subject:* Re: [Freesurfer] Clusters locations > > Hi Antonella, what level of detail do you want? I think that most > people are reporting MNI coordinates. > doug > > On 2/13/12 2:44 PM, Antonella Kis wrote: >> Hi Doug, >> >> I will be very grateful if you give me some directions regarding how >> I can get my clusters location ( my output is too general telling me >> just Left-Cerebral-White-Matter and Right-Cerebral-White-Matter) and >> the coordinates (MNI) when I run the: >> >> mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask >> GroupAnalysis_pos.glmdir/mask.mgh --no-fixmni --cwsig >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh >> .09 --seg cvs_avg35 aseg.mgz --csdpdf >> GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd >> GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh >> >> and >> >> >> mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i >> /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.nii.gz >> >> --avgwf fa.avg.dat --sum permcsd.sig.cluster.summary >> >> >> Thank you. >> Antonella > > _______________________________________________ > 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 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
