Hi Doug,
By "more exactly location" I want to say that I would like to have the MNI coordinates and also the annotation location or the nearst cortical label (for example precentral or lateraloccipital, etc). Also,after I ran the mri_segstatsI don't have the MNI coordinates.
Thanks for helping. Antonella
From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 14, 2012 1:18 PM Subject: Re: [Freesurfer] Clusters locations
Antonella Kis wrote:
Hi Doug,
- 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.
- 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 greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@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.