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.eduwrote:

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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list 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.

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.eduwrote:

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.edumailto: 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

...

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

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

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.eduwrote:

...

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.edumailto: 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

...

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

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

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.eduwrote:

...

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.eduwrote:

...

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 _______________________________________________ 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

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

---

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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

Hi,

I made a label for the rest of the brain. In the colour table, I put 0 0 0 and 0 for opacity. This may make the desired annotation transparent, but the rest of the original brain is still grey. Is there a way to not view the original brain surface? Or to change the colour?

Thanks, Allie

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.commailto: 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