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 <gr...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@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,
>
> 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
_______________________________________________
Freesurfer mailing list
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.
