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: > > 1) 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. > > 2) 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
