Hi, Please ignore the previous question. I seem to have figured it out... for now.
Thanks, Allie On Wed, Mar 9, 2011 at 2:29 PM, Allie Rosen <rosen.al...@gmail.com> 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> 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>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>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>> 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 >>> >>>>> >>> >>>> >>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>> >>> >>> >>> >>> _______________________________________________ >>> >>> Freesurfer mailing list >>> >>> 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 >>> >> 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 >>> >> >>> >> >>> > >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> >
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