use mri_aparc2aseg instead of label2vol. This is how aparc+aseg.mgz is created. Look in the recon-all.log file for the command line used.
doug On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote: > Hi all, > > I want to convert the cortical labels I get in freeSurfer to volumetric > ROIs in the subject space and I've followed the steps mentioned in: > http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ > > except since I'm interested in lobe mapping I've changed the first > commands, more specifically these are the different command I've run: > > 1. mri_annotation2label --subject P2 --hemi lh --outdir > freeSurfer_Results/P2/labels/ --lobesStrict > freeSurfer_Results/P2/labels/freeSurfer_lobes > > 2. mri_annotation2label --hemi lh --subject P2 --outdir > freeSurfer_Results/P2/labels/ --annotation > freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot > > 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s > P2 --regheader --reg freeSurfer_Results/P2/register.dat > > 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label > --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o > freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 > --fillthresh 1 --reg freeSurfer_Results/P2/register.dat > > the issue I have now is that the final ROI I get (e.g. > "lh.parietal.nii.gz") looks like a series of disconnected points! I was > wondering how I can get a smooth (i.e. filled) volumetric ROI? > > Thanks, > -Mojdeh > > _______________________________________________ > 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.
