From justintbaker@gmail.com Fri Dec  9 15:08:35 2011
From: Justin Baker <justintbaker@gmail.com>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tcl script question: labl_set_color
Date: Fri, 09 Dec 2011 15:08:32 -0500
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 <CAJ0pNgz01xp3nd9cAF71WT9cchFm8TtQMJhVWmr_=FqvKrFaqQ@mail.gmail.com>
In-Reply-To: <alpine.LRH.2.00.1112051507190.23932@gate.nmr.mgh.harvard.edu>
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OK, right-clicking on the surface did in fact de-select the label (turning
it all to a uniform color).  Way to script a right-click?  (I see left
click...)

Now that this is more or less working, I am looking to do something
slightly different: i.e., combine the boundaries of one set of regions, one
highlighed region, and an activation map.  Is there a way to fill just one
label and leave outlines for a different set of labels in the same image?
Or alternatively set a different outline color for one label?  As in my
previous post, I am looking to do this via tcl script if possible.

Thanks.


On Mon, Dec 5, 2011 at 3:07 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wr=
ote:

> yes, just use the -tcl <script name> option, but don't but an "exit"
> command at the end of the tcl script
>
> cheers
> Bruce
>
> On Mon, 5 Dec 2011, Justin Baker wrote:
>
>  Ah - in that case I have a total newbie question, since I primarily use
>> tksurfer via command line:
>>
>> Is there a way to load up a case using the tcl script, but then leave it
>> open rather than quit?
>> This way I could try de-selecting with right-click.
>>
>> Thanks.
>>
>> On Mon, Dec 5, 2011 at 9:05 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>
>> wrote:
>>      I think so, but I want to see if it fixes your problem before I go
>> digging through the
>>      tcl code to see what it is
>>      On Mon, 5 Dec 2011, Justin Baker wrote:
>>
>>            Is there a command to do this via tcl script?
>>
>>            Justin
>>
>>            On Sun, Dec 4, 2011 at 8:49 PM, Bruce Fischl <
>> fischl(a)nmr.mgh.harvard.edu>
>>            wrote:
>>                 What happens if you right click on the surface then?
>>
>>
>>
>>            On Dec 4, 2011, at 8:17 PM, Justin Baker <
>> justintbaker(a)gmail.com>
>>            wrote:
>>
>>                 Hi Bruce,
>>
>>                 Thanks.  Some progress!  That resulted in the label border
>>                 turning red, but the fill is still white.  Any other
>>                 thoughts?
>>
>>                 Cheers,
>>                 Justin
>>
>>                 On Wed, Nov 30, 2011 at 2:54 PM, Bruce Fischl
>>                 <fischl(a)nmr.mgh.harvard.edu> wrote:
>>                       Hi Justin
>>
>>                       try unselecting the label with:
>>
>>                       labl_select -1
>>
>>                       cheers
>>                       Bruce
>>                       On Wed, 30 Nov 2011, Justin Baker wrote:
>>
>>
>>                             I am trying to use tksurfer to
>>                             script overlay of a label +
>>                             functional map
>>                             onto an fsaverage5 surface.
>>
>>                             In particular, I want to set the
>>                             label to "fill" and color it red.
>>
>>                             I have:
>>
>>                             set labelstyle 0
>>                             labl_set_color 0 255 0 0
>>
>>                             As you can see below, the output
>>                             of label_print_list shows that the
>>                             color of
>>                             the label should be "255 0 0 " but
>>                             it looks white in the output
>>                             image.
>>
>>                             Am I missing something?  Thanks
>>
>>                             ------------
>>                             subject is fsaverage5
>>                             hemi    is lh
>>                             surface is inflated
>>
>>                             Label 0
>>                                    Name:
>>                             lh.17Networks_LH_ContB_PFClv.**label,
>>                             109 vertices
>>                                    Structure: -1 Color: 255 0
>>                             0 Visible: 1
>>                                    Bounds: x -20.879234
>>                             12.792567 y -4.000000 109.853737 z
>>                             -4.033233
>>                             4.040778
>>
>>
>>
>>
>>
>>
>>
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>>
>>
>>



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From fischl@nmr.mgh.harvard.edu Fri Dec  9 16:05:49 2011
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tcl script question: labl_set_color
Date: Fri, 09 Dec 2011 16:05:48 -0500
Message-ID: <alpine.LRH.2.00.1112091554240.25952@gate.nmr.mgh.harvard.edu>
In-Reply-To:
 <CAJ0pNgz01xp3nd9cAF71WT9cchFm8TtQMJhVWmr_=FqvKrFaqQ@mail.gmail.com>
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I think you can set the outline color of each label indepently by using=20
it's index which is assigned in the order in which it is loaded I believe.=20
So in our example below =C2=A0labl_set_color 0 255 0 0, change the first "0" =
to=20
a "1" for the second label. Also, I would have thought labl_select -1 would=20
deselect the label and turn off the white marks, but if not you can also=20
try calling clear_all_vertex_marks in the tcl script


On Fri, 9 Dec 2011, Justin Baker wrote:

> OK, right-clicking on the surface did in fact de-select the label (turning
> it all to a uniform color).=C2=A0 Way to script a right-click?=C2=A0 (I see=
 left
> click...)
>=20
> Now that this is more or less working, I am looking to do something slightly
> different: i.e., combine the boundaries of one set of regions, one
> highlighed region, and an activation map.=C2=A0 Is there a way to fill just=
 one
> label and leave outlines for a different set of labels in the same image?=
=C2=A0
> Or alternatively set a different outline color for one label?=C2=A0 As in my
> previous post, I am looking to do this via tcl script if possible.
>=20
> Thanks.
>=20
>=20
> On Mon, Dec 5, 2011 at 3:07 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>
> wrote:
>       yes, just use the -tcl <script name> option, but don't but an
>       "exit" command at the end of the tcl script
>
>       cheers
>       Bruce
>       On Mon, 5 Dec 2011, Justin Baker wrote:
>
>             Ah - in that case I have a total newbie question,
>             since I primarily use tksurfer via command line:
>
>             Is there a way to load up a case using the tcl
>             script, but then leave it open rather than quit?=C2=A0
>             This way I could try de-selecting with right-click.
>
>             Thanks.
>
>             On Mon, Dec 5, 2011 at 9:05 AM, Bruce Fischl
>             <fischl(a)nmr.mgh.harvard.edu> wrote:
>             =C2=A0 =C2=A0 =C2=A0I think so, but I want to see if it fixes y=
our
>             problem before I go digging through the
>             =C2=A0 =C2=A0 =C2=A0tcl code to see what it is
>             =C2=A0 =C2=A0 =C2=A0On Mon, 5 Dec 2011, Justin Baker wrote:
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Is there a command to =
do this via tcl
>             script?=C2=A0
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Justin
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0On Sun, Dec 4, 2011 at=
 8:49 PM, Bruce
>             Fischl <fischl(a)nmr.mgh.harvard.edu>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0wrote:
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Wh=
at happens if you right click on
>             the surface then?
>=20
>=20
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0On Dec 4, 2011, at 8:1=
7 PM, Justin Baker
>             <justintbaker(a)gmail.com>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0wrote:
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Hi=
 Bruce,
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Th=
anks.=C2=A0 Some progress!=C2=A0 That
>             resulted in the label border
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0tu=
rning red, but the fill is still
>             white.=C2=A0 Any other
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0th=
oughts?
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Ch=
eers,
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Ju=
stin
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0On=
 Wed, Nov 30, 2011 at 2:54 PM,
>             Bruce Fischl
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0<f=
ischl(a)nmr.mgh.harvard.edu> wrote:
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0Hi Justin
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0try unselecting the label
>             with:
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0labl_select -1
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0cheers
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0Bruce
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0On Wed, 30 Nov 2011, Justin
>             Baker wrote:
>=20
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0I am trying to use
>             tksurfer to
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0script overlay of a
>             label +
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0functional map
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0onto an fsaverage5
>             surface.
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0In particular, I want to
>             set the
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0label to "fill" and
>             color it red.
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0I have:
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0set labelstyle 0
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0labl_set_color 0 255 0 0
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0As you can see below,
>             the output
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0of label_print_list
>             shows that the
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0color of
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0the label should be "255
>             0 0 " but
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0it looks white in the
>             output
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0image.
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Am I missing something?=C2=A0
>             Thanks
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0------------
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0subject is fsaverage5
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0hemi =C2=A0 =C2=A0is lh
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0surface is inflated
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Label 0
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0Name:
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
>             =C2=A0lh.17Networks_LH_ContB_PFClv.label,
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0109 vertices
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0Structure=
: -1
>             Color: 255 0
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00 Visible: 1
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0Bounds: x
>             -20.879234
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A012.792567 y -4.000000
>             109.853737 z
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0-4.033233
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A04.040778
>=20
>=20
>=20
>=20
>=20
>=20
>
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0The information in thi=
s e-mail is
>             intended only for the
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0person to whom it is
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0addressed. If you beli=
eve this e-mail was
>             sent to you in
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0error and the e-mail
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0contains patient infor=
mation, please
>             contact the Partners
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Compliance HelpLine at
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://www.partners.or=
g/complianceline .
>             If the e-mail was
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0sent to you in error
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0but does not contain p=
atient information,
>             please contact
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0the sender and properly
>             =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0dispose of the e-mail.
>=20
>=20
>=20
>=20
>=20
>=20
>=20
>=20
>

--===============8514557701466773389==--