I would just use the 2nd command since aparc.a2009s+aseg.mgz will have already resolved the issues of overlap that you mention. doug
On 07/02/2015 04:07 AM, Martin Hebart wrote: > Here's the exact code that I used: > > surface: > mri_label2vol --annot aparc.a2009s.annot --regheader > $1/$2/mri/orig.mgz --o $1/$2/roi/mask_lh.nii --temp $1/$2/mri/orig.mgz > --subject $2 --hemi lh --proj frac 0 1 .1 > > same for the right hemisphere. > > volumetric: > mri_label2vol --seg $1/$2/mri/aparc.a2009s+aseg.mgz --regheader > $1/$2/mri/orig.mgz --o $1/$2/roi/mask_vol.nii --temp > $1/$2/mri/orig.mgz --subject $2 > > Cheers, > Martin > > > 2015-07-01 23:38 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > > How did you create the ROIs? > > On 07/01/2015 12:25 PM, Martin Hebart wrote: > > Dear members of the list, > > > > I'm new to Freesurfer, so please excuse me asking possibly basic > > questions. I have spent quite some time on the wiki and searching > > through the emails before writing to the list, but I might have > missed > > some important information. > > > > I would like to work on anatomical ROIs created based on > Freesurfer's > > surface-based and volumetric ROIs and continue working with them in > > nifti format (e.g. for SPM). If I understand it correctly, the > > surface-based ROIs should take into account the individual subject's > > anatomy better than the volumetric ROIs would. At the same time, for > > subcortical regions it is necessary to use volumetric ROIs. > > > > I did recon -all, followed by extracting all surface ROIs using > > mri_label2vol --annot aparc.a2009s.annot and the volumetric ROIs > using > > mri_label2vol --seg aparc.a2009s+aseg.mgz . Finally, I manually > > removed all cortical labels from the volumetric ROIs. > > > > Now when looking at the ROIs, they overlap slightly, both > between left > > and right hemisphere (roughly 150 voxels), and between the > hemispheres > > and the subcortical regions (roughly 300 voxels). > > > > Is there a way I can assign the masks volumes a unique label? I was > > considering removing these voxels, but ideally I would just keep > them > > in and use the label with the highest probability. Or is there an > > alternative suggestion that makes more sense (e.g. rather > attributing > > overlapping regions to subcortical regions)? > > > > Thanks a lot in advance for your reply! > > Martin > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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. > > > > > _______________________________________________ > 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
