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 (Class1Class2)?
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
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