On Wed, Mar 9, 2011 at 2:35 PM, Allie Rosen <rosen.allie@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 <greve@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.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
<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
>>
>> greve@nmr.mgh.harvard.edu <mailto:greve@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
greve@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