Hi Leise the numbers come from our color lookup file that is in $FREESURFER_HOME/FreeSurferColorLUT.txt
cheers Bruce On Mon, 6 Oct 2014, Leise Borg wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
