For recon-all (the stable3 version), you should use the index (col, row, slice), not a mm RAS (if you are passing them on the cmd line).
doug
Fornito, Alexander wrote:
I'll give it a try. What should the input and output vols be if I want to use the coords to place seed points? Does it matter which vol I use?
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
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 4/6/2006 11:03 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] MNI coords
Hi Alex,
you should get the MNI coords for all your subjects - recon-all runs the MNI talairach procedure. Did you move things around on disk? I think there are times that it can't find the xform anymore because it is in a different location than when you ran recon-all. See if there is a talairach.xfm in the subjects mri/transforms directory for one of the ones you don't get MNI coords. If it's there and you're not getting MNI coords, try using
mri_add_xform_to_header <full path to talairach.xfm> <input vol> <output vol>
cheers, Bruce
On Thu, 6 Apr 2006, Fornito, Alexander wrote:
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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