Hi Douglas Thanks for your answers. I have two more questions: 1) In which file(s) do I find the labels 151-255? 2) What do the columns of zeros and the numbers 64, 112, 160, 208 and 255 in your answer mean?
Leise -----Original Message----- From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: 4. oktober 2014 18:22 To: Leise Borg; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter and white matter lesions 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: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. 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
