Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere.
doug Prapti Gautam wrote: > 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 _______________________________________________ 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.
