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.ozra...@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 -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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.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.ozra...@childrens.harvard.edu<mailto:olga.ozra...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. 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-palc...@tch.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
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