Hi Ola, you'll need to get the MNI VBM results from MNI space back into your individual subject space somehow. This will involve applying the inverse transform. I don't know how to do that with SPM/VBM.
doug
ps. If you or someone else knows how, please post tothe list
On 06/05/2013 11:19 AM, Ozranov-Palchik, Ola wrote:
MNI space.
On Jun 5, 2013, at 11:14 AM, Douglas N Greve wrote:
what space is your VBM map in? doug
On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote:
Hi Doug,
Thank you for your response! I am still a bit confused about the vol2surf command. I have a volumetric mask with voxels of interest based on a VBM analysis in SPM. I would like to extract the cortical thickness measurements based on these voxels. I am not clear what specifications I need to include when using vol2surf. For example, what do I use as my registration matrix?
Thank you for your help! Ola
Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozranov@childrens.harvard.edu mailto:olga.ozranov@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, June 04, 2013 1:48 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness
Make sure that your SPM volume is registered to the anatomical, then use mri_vol2surf to map the volume to the surface, then mri_segstats to extract the mean of the thickness
doug
On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote:
main lab: (617) 355-0400
Dear FreeSurfer Experts,
I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer.
Thank you in advance for your help!
Ola
Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience
Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozranov@childrens.harvard.edu mailto:olga.ozranov@childrens.harvard.edu mailto:olga.ozranov@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Ola Ozranov-Palchik, M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 Ola.Ozranov-Palchik@tch.harvard.edu mailto:olga.ozranov@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab