Hi Doug, I used --help. I loaded the annotation but the other regions were still all present. This makes me think that I need to have ALL areas of the brain included in the colour table, with values of 0 for the colours, or values of 100 for opacity. I'll give this a shot.
Thanks, Allie On Wed, Mar 9, 2011 at 2:32 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > The idea is that you copy it into one location (no need to make multiple > copies), then modify it to match what you want. You'll need to change the > names at least. Try running it with --help to get more info. And, yes, you > can make your own label! > > doug > > > > Allie Rosen wrote: > >> Hi Again, >> >> I made a label on my own instead of using annotation2label. First, is this >> even allowed? >> >> Now I am trying to use label2annot. I'm not sure how to specify the colour >> table. I typed in: "--ctab FreeSurferColourLUT.txt but it can't find the >> file. I found it in the freesurfer home file, and copied it into my subject >> directory, and into the individual subject's file. Should I put it somewhere >> else? Is that even the correct file? >> >> Thanks! >> Allie >> >> >> >> >> On Wed, Mar 9, 2011 at 2:12 PM, Allie Rosen <rosen.al...@gmail.com<mailto: >> rosen.al...@gmail.com>> wrote: >> >> My lab doesn't have matlab... I'll work on the label2annot and >> annotation2label programs. >> >> Thanks, >> Allie >> >> >> >> >> On Wed, Mar 9, 2011 at 2:02 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> >> >> wrote: >> >> we don't have any tools for doing so, but you could do it in >> matlab >> On Wed, >> 9 Mar 2011, Allie Rosen wrote: >> >> > Hi, >> >> > Can I modify the colour table of an annotation file? >> Apparently there is an >> > embedded colour table in annotation files. >> > >> > Allie >> > >> > >> > >> > On Wed, Mar 9, 2011 at 1:07 PM, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>wrote: >> > >> >> It will eliminate them from the annotation which should >> mean that those >> >> areas should be transparent. >> >> doug >> >> >> >> Allie Rosen wrote: >> >> >> >>> Hi Doug, >> >>> >> >>> Thanks for the response. Do those commands make the >> annotations/labels >> >>> transparent? >> >>> >> >>> Allie >> >>> >> >>> >> >>> >> >>> On Tue, Mar 8, 2011 at 10:58 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu><mailto: >> >> >>> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >>> >> >>> I've never used that, but you can use >> mris_annotation2label to >> >>> break the annotation in to individual labels,then use >> >>> mris_label2annot to put the ones you want back together. >> >>> >> >>> doug >> >>> >> >>> >> >>> On 3/8/11 10:13 PM, Allie Rosen wrote: >> >>> >> >>>> Hi Everyone, >> >>>> >> >>>> I'm wondering if it is possible to use the "cut" >> function in >> >>>> TkSurfer to delete specific atlas annotations. For >> example, can I >> >>>> create a label of my specific area of interest, >> inverse the label >> >>>> to highlight the rest of the brain, and then either >> cut out these >> >>>> regions or make them transparent? >> >>>> >> >>>> Can anyone help me out? >> >>>> >> >>>> Thank you, >> >>>> >> >>>> Allie Rosen, MSc >> >>>> Graduate Student, Department of Neurosurgery >> >>>> Toronto Western Hospital 14-327 399 Bathurst St. >> >>>> University of Toronto >> >>>> _______________________________________________ >> >>>> Freesurfer mailing list >> >>>> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >>>>> >> >>>> >> >>>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>> >> >>> >> >>> _______________________________________________ >> >>> Freesurfer mailing list >> >>> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >>> >> >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>> >> >>> >> >>> 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 <mailto:gr...@nmr.mgh.harvard.edu> >> >> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> >> >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >
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