On 01/10/2014 11:40 AM, sujith vijayan wrote:
Hi All
I am using wmparc.mgz and aparc.a2009s+aseg.mgz to determine the closest grey matter region for electrodes in some human epileptic patients; I have the RAS coordinates of the electrodes. I have a couple of questions:
- When the electrode (its RAS coordinate) is close to the midline and
out of the grey matter it won't give me the closest grey matter label (like wmparc does with the white matter). Is there someway to get this in a principled manner? For example, is there a way to get a file with all the RAS coordinates and the parcellation labels, so I could find the closest neighbor in Matlab?
If you make a label file with the surface RAS coordinates of the electrodes, you can run run mri_label2label specifying the same subject as the source and target and --regmethod surface and --paint and it will map the points to the closest surface point.
- The recons for three subjects were done between 2008 and 2010 using
freesurfer. Therefore files like aparc.a2009s+aseg.mgz, wmparc.mgz, lh.aparc.a2009s.annot are missing. Is there a simple way just to recreate these set of files (one command would be great, even if it takes a little bit of time)? Or does the entire recon have to be done again?
If you have an installation of FS 5.3, you can run recon-all -s subject -wmparc -cortparc2 -aparc2aseg I think this will work on a 5.0 folder. I would make a copy of your subject before running it. It will regenerate the aparc+aseg.mgz file
doug
Thanks,
Sujith
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