Re: [Freesurfer] Aparc Cutting?

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.allie@gmail.com mailto:rosen.allie@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
<fischl@nmr.mgh.harvard.edu <mailto:fischl@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
    > <greve@nmr.mgh.harvard.edu
    <mailto:greve@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
    <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu><mailto:
    >>> greve@nmr.mgh.harvard.edu
    <mailto:greve@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
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    <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    >>>>>
    >>>>
    >>>>  
     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >>>>
    >>>
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    <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>
    >>>
    >>>  
     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >>>
    >>>
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    >> --
    >> Douglas N. Greve, Ph.D.
    >> MGH-NMR Center
    >>
    >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    >> Phone Number: 617-724-2358 Fax: 617-726-7422
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