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>: > 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 > > 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. > >
_______________________________________________ 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.
