Hi David, you can use mri_label2vol with the --proj option. This works ok, but it is often not great. Another way (the way that aparc+aseg) is created is to convert your label into an annotation, then use mri_aparc2aseg.
doug On 10/31/11 7:22 PM, David Grayson wrote: > Hi Doug, > > Although in principle, yes this is the idea, we have a set of labels that > aren't actually in the aparc+aseg file (basically a set of high-density > subdivisions of those regions). The only problem is that the labels I have > are just in "surface-land." I am wondering, once I have the surface labels, > is there a way to re-propagate them back into the gray matter? > > Thanks again, > > David > > -----Original Message----- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Monday, October 31, 2011 2:38 PM > To: David Grayson > Cc: 'freesurfer@nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] propagating labels to gray matter > > Do you just want the label in the orig volume space? If so, just use the > labels in aparc+aseg.mgz > doug > > David Grayson wrote: >> Hi Doug, >> >> /path/to/FREESURFER/label/regenerated_lh_36$ mri_label2vol --label >> lh.bankssts.label --temp ../../mri/orig.mgz --identity --o TEST.nii.gz >> >> Thanks, >> >> David >> >> -----Original Message----- >> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >> Sent: Monday, October 31, 2011 2:04 PM >> To: David Grayson >> Cc: 'freesurfer@nmr.mgh.harvard.edu' >> Subject: Re: [Freesurfer] propagating labels to gray matter >> >> what was your label2vol command line? >> doug >> >> David Grayson wrote: >> >>> Hi freesurfer experts, >>> >>> >>> >>> I currently have a set of cortical labels that are the result of a >>> high-resolution parcellation of the standard aparc.annot labels (via >>> the ‘connectomemapper’ software). I would like to extract the gray >>> matter ROIs that correspond to these labels, and I understand that >>> this requires a method to ‘propagate’ these labels through the gray >>> matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to >>> only give me that pial or white surfaces, as opposed to the gray >>> matter bodies. Does anyone know how to accomplish this? >>> >>> >>> >>> Thank you very much, >>> >>> >>> >>> David Grayson >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> _______________________________________________ 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.
