You will need to create a new color table. It is currently referencing FreeSurferColorLUT.txt. If you load the segmentation as both a segmentation and the aux volume, you can see the number associated with the color. You will need to create a table similar to FreeSurferColorLUT.txt doug
On 05/28/2013 01:51 PM, Gonzalo Rojas Costa wrote: > Hi Doug: > > It is labeled as wm-rh-fusiform and wm-lh-fusiform > > Sincerely, > > > > Gonzalo Rojas Costa > > On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: >> what is is labled? >> >> On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: >>> Hi Doug: >>> >>> I use the instructions that you told me... But, why I get the gray >>> colored region (red arrow) ?... >>> >>> Sincerely, >>> >>> >>> Gonzalo Rojas Costa >>> >>> >>>> Message: 15 >>>> Date: Mon, 27 May 2013 22:41:41 -0400 >>>> From: Douglas Greve <gr...@nmr.mgh.harvard.edu> >>>> Subject: Re: [Freesurfer] white matter volume per lobe... >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Message-ID: <51a41965.6050...@nmr.mgh.harvard.edu> >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>> >>>> you will need to run mri_annotation2label and specify the output to be >>>> an annotation file instead of a segmentation. Then you will have to run >>>> mri_aparc2aseg, specifying your lobes annotation as well as --labelwm >>>> (look in the recon-all.log file for an example of how wmparc.mgz is >>>> created). Then run mri_segstats (you can also get an example from the >>>> recon-all.log file). >>>> doug >>> -- >>> Gonzalo Rojas Costa >>> Laboratory for Advanced Medical Image Processing >>> Department of Radiology >>> Clínica las Condes >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>> Tel: 56-2-2105170 >>> Cel: 56-9-97771785 >>> www.clc.cl >> >> -- >> 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. >> > > -- 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
