Hi Antonella, I have created a registration file that will allow you to get coordinates (this one assume that you performed your group analysis in CVS space). ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg.cvs-to-fsaverage.dat You can pass this to mris_volcluster. This will allow volcluster to report the segmentation that the peak falls into, but this will not tell you the closest cortical label. I'm working on a solution to that for the CVS subject.
doug
Antonella Kis wrote:
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 nearest cortical label (for example precentral or lateraloccipital, etc). Also,after I ran the mri_segstats I 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
mailto:greve@nmr.mgh.harvard.edu>
*To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com>;
free surfer
<freesurfer@nmr.mgh.harvard.edu mailto: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
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