That is just a color lookup table that has an exhaustive list of possible regions. We do not label all of these, and some of them appear in some segmentations and not in others. I don't know who (or what program) does that thalamus labeling (it is not part of a2005s). It is probably part of the tract-based labeling that Zeynep Saygin does. doug
Kern, Mark wrote: > Hi Doug, > > I must be misunderstanding the contents of the a2005s. From the LUT at > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT, > there is a section under the color table listing for the a2005s for index > numbers in the 7000's and 8000's that list thalamic and subcortical regions. > If these indices are not part of the a2005s scheme, are they available in any > other segmentation schemes? > Thanks for considering this matter. > > Best, > Mark > > > ________________________________________ > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Thursday, March 08, 2012 10:37 AM > To: Kern, Mark; freesurfer > Subject: Re: [Freesurfer] aparc.a2005s+aseg.mgz > > Hi Mark, I don't think thalamic structures were part of the a2005s. I > think it was only cortical structures. The aparc.a2005s+aseg.mgz will > have a whole thalamus segmentation, but that is inherited from the aseg.mgz > doug > > Kern, Mark wrote: > >> Hi Doug, >> >> Yes, the aparc.a2009s+aseg.mgz files were created and I have used them in a >> great deal of our analysis of large scale network connectivity of cerebral >> cortical regions. We have a desire to look at some subcortical structures >> that are part of the a2005s scheme but not included in the a2009s treatment, >> especially the subdivision of the thalamus. Any help in this matter would >> be greatly appreciated. >> >> Best Wishes, >> Mark >> >> >> On Mar 7, 2012, at 10:47 PM, Douglas Greve wrote: >> >> >> >>> Hi Mark, was aparc.a2009s+aseg.mgz created? That is the new one. >>> doug >>> >>> On 3/7/12 8:43 AM, Kern, Mark wrote: >>> >>> >>>> Dear Freesurfer Mavens, >>>> >>>> After running "recon-all -all" on a set of anatomical data, I wished to >>>> used the aparc.a2005s+aseg.mgz in a connectivity analysis pipeline to >>>> create some ROI masks. I was particularly interested in the subcortical >>>> regions contained in the a2005s scheme. However, the >>>> aparc.a2005s+aseg.mgz file was not created during the recon-all processing >>>> run. Is there a way to get the a2005s segmentation data? >>>> >>>> Thanks for your help. >>>> >>>> Best, >>>> >>>> Mark >>>> >>>> Senior Research Scientist >>>> Division of Gastroenterology and Hepatology >>>> Departmernt of Medicine >>>> Medical College of Wisconsin >>>> Milwaukee, WI >>>> _______________________________________________ >>>> 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. >>> >>> >>> >> >> >> > > -- > 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 > > > > -- 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
