Hi, I made a label for the rest of the brain. In the colour table, I put 0 0 0 and 0 for opacity. This may make the desired annotation transparent, but the rest of the original brain is still grey. Is there a way to not view the original brain surface? Or to change the colour?
Thanks, Allie On Wed, Mar 9, 2011 at 2:35 PM, Allie Rosen <rosen.al...@gmail.com> wrote: > 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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