Hi David, an easy way is to load the segmentation as both a segmentation and as the auxiliary volume (not aux segmentation). When you click on a point, you'll see the number of the segmentation in the aux field of the control window. doug
David Grayson wrote: > Hi Doug, > > I made good progress based on your suggestion of using mri_aparc2aseg. The > last piece is that I need to understand what the index values of my output > volume file correspond to. Here's the command I used: > > mri_aparc2aseg --s subID --annot myaparc --o TEST.nii.gz > > Although I did notice that the index values in TEST.nii.gz for the cortical > ROIs in the RH are just above 2000, and just above 1000 for the LH, the > values don't seem to match the labels in FreeSurferColorLUT.txt. Then again, > that makes sense, because this is a custom label set, so they don't really > exist in FreeSurferColorLUT.txt. > > How can I learn more about how the index values are being assigned? > > Thanks very much for your help, > > David > > P.S. I don't know if it will work, but I attached the aparc and volume files > if it's necessary for you to look that those > > -----Original Message----- > From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Monday, October 31, 2011 7:40 PM > To: David Grayson > Cc: 'freesurfer@nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] propagating labels to gray matter > > 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 >>>> >>>> > > > 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. > -- 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
