So - just to be sure - if I take labels 2, 7, 41, and 46 from aseg.mgz, then I have ALL white matter in the entire brain?
And another question: I also need the white matter hypointensities. Until now, I used label 77 of aparc.a2009s+aseg.mgz. Is that sufficient? Or should I use the aseg.mgz file for this too? -Leise -----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: 3. oktober 2014 18:55 To: Leise Borg; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter and white matter lesions Those are the only WM labels present in the aseg. You may or may not want to include brain stem as WM. On 10/03/2014 04:03 AM, Leise Borg wrote: > > Hi again > > Labels 7 and 46 in the aseg-file gives me the cerebellum white matter > - which I can see from the aseg.stat-file. From the list at > http://www.slicer.org/slicerWiki/index.php/Slicer3:Freesurfer_labels I > can see that I also need the labels 2 and 41. It looks ok to me when I > plot it, but can I be sure that it gives me all white matter (NOT > white matter hypointensities)? I can see that there are several other > labels referring to white matter, such as label 219, 223, 3000 etc. Do > those labels point at subsets of the labels 2 and 41 (and 7 and 46)? > > -Leise > > *From:*Leise Borg > *Sent:* 3. oktober 2014 08:48 > *To:* 'gr...@nmr.mgh.harvard.edu' > *Subject:* Re: [Freesurfer] White matter and white matter lesions > > Hi Douglas > > Thanks a lot for your answer. I will definitely do that. Can you tell > me how I load this aseg.stats file into Matlab? I do not have > FreeSurfer downloaded on my own computer. Do I need that to load this > file? > > -Leise. > > Why not just use the values in aseg.stats? > > On 10/01/2014 07:44 AM, Leise Borg wrote: > > > > > > Hi FreeSurfer > > > > > > I am working on a project concerning Alzheimer's patients and I need > > > to know the positions of white matter (WM) and white matter lesions > > > (WML) from your segmentations. > > > > > > To find the WML, I use label 77 in the aparc.a2009s+aseg.mgz-files. > > > > > > To find the WM, I use labels 2 and 41 in the ribbon.mgz-files and > > > subtract the ventricles by subtracting labels: 4, 5 14, 15, 43 44 > > > found in the aseg.mgz-files. > > > > > > However, in the two sets of positions - one for WML and one for WM > > > -there is an overlap. It is not big, but it is there. > > > > > > Can you help me finding the true WML- and WM-segmentations? > > > > > > With kind regards, Leise. > -- 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/ 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
