Hi Bruce, I tried using the volume scanner coords (which were identical to the RAS coords), but this didn't seem to do the trick; the cutting plane was still skewed away from the true midline. After re-running some of my images using the volume scanner coords, I've noticed that I now have the MNI coords. However, I still didn't get them for some images. Is there a flag or command that I can specify to ensure that I do obtain the MNI coords? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 3/30/2006 11:41 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MNI coords
Hi Alex,
try "volume scanner coords" for the subjects that don't have the MNI coords. Sorry, I know this is more confusing than it needs to be. In the new version you just specify voxel coords :)
Bruce On Thu, 30 Mar 2006, Fornito, Alexander wrote:
Hi, I need to manually specify a seed point for the corpus callosum cutting plane on some of my images, although some of them don't seem to have the MNI coordiates available through clicking view >information in tkmedit. Not sure why this is the case, since other images do have this info. Specifying the RAS coord doens't fix the problem. I'm using recon-all version 1.104 2005/09/07 (I'm trying to finish off a study using the dev version and wold dearly like to avoid re-processing everyone with a newer version!!). Any help is much appreciated. Many thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
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