Here is the original thread (to at least most of it). Maybe I am just an idiot, but I cant' figure out how to easily reply from the web to an entire thread, and pulling it out of the digests I get is a pain!!
They wanted to take an ROI from SPM and put it into free surfer to extract cortical thickness. I thought going through fsaverage was a good way to do this. But as I said, looking at the surface, I have some concerns. I am more confused by when you tell them to run the MNI template through recon-all to get a surface, because I thought fsaverage was a kind of MNI space that has already been run through?
Thanks, Stephanie
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.ozra...@childrens.harvard.eduhttp://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-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, June 04, 2013 1:48 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.ozra...@childrens.harvard.eduhttp://childrens.harvard.edu mailto:olga.ozra...@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab
Then it goes on:
Hi Ola, this probably will not work. The tal coordinate is notoriously inaccurate in cortex. You are verylikely to totally miss the area you are looking for. A better way is to run the MNI template through recon-all, map your VBM result to the surface of that, then use mri_surf2surf to map the effect to each individual.
doug
On 06/05/2013 02:58 PM, Ozranov-Palchik, Ola wrote:
Hi Doug,
Thank you, again! I decided to try to use the Talairach coordinates from my analysis for ROI extraction. I created an average subject and preprocessed the data (mris_preproc). I obtained the vertex index based on the coordinates from the average subject. Any ideas on how I can now find the corresponding vertices in all my subjects?
Thanks very much! Ola
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422