On Wed, Mar 9, 2011 at 2:29 PM, Allie Rosen <rosen.allie@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.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> 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>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>> 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
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>>>>>
>>>>
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>>>>
>>>
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>>
>> greve@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
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