On 10/4/14 12:35 AM, Leise Borg wrote:
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?
You should also add 251-255 251 CC_Posterior 0 0 64 0 252 CC_Mid_Posterior 0 0 112 0 253 CC_Central 0 0 160 0 254 CC_Mid_Anterior 0 0 208 0 255 CC_Anterior 0 0 255 0
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?
That is sufficient
-Leise
-----Original Message----- From: Douglas N Greve [mailto:greve@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:* 'greve@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.