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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