Hi Doug, Thanks for the reply. I have tried using the method you've suggested, however, I'm stuck because mri_label2annot which I use to turn my label into a annot file only works in one hemisphere while mri_aparc2aseg works for the whole brain. Do you know a work around for this?
Can I merge the annot files created from each hemisphere so that I can pass it to mri_aparc2aseg? Thanks, Prapti -----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, 16 September 2010 1:34 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues The problem is that mri_label2volume just does not work all that well on surface labels. Another way to do this is to create an annotation from the single label using mris_label2annot, then create a segmentation/mask volume using mri_aparc2aseg. doug Prapti Gautam wrote: > > Dear freesurfers, > > I am trying to convert a label that I have hand drawn into tksurfer > into a volume file using mri_label2volume and succeed in transforming > into a volume file but the volume looks splotchy and the ends are not > connected , i.e. instead of a smooth bit of cortex I get disjointed > bits in the cortex.. I found a similar problem being discussed > previously in the archives > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01999.htm l) > but I can't seem to find the solution to it myself. > > The steps I've used are: > > Draw label in tksurfer, and save it and then use the following command. > > mri_label2vol --label test.label --temp norm.mgz -- reg > mni152.register.dat -- proj abs 0 1 0.1 --subject --hemi lh --o > test.label.mgz > > When I load the resultant volume file, the surface is not smooth and > there are holes in the surface. I've tried changing the delta values > to quite small as well as setting the thickness at 2 with - - proj abs > option, but this hasn't made things better.. > > Has anyone encountered this problem before and knows how to solve it ? > Am I missing something in the syntax? > > Thanks very much in advance, > > Prapti > > ------------------------------------------------------------------------ > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
