Doug,

Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled?

I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case...

Best, Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 2/26/14 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

I'm not sure about freeview, but you cannot do it in tksurfer. You can take your two labels and create an annotation with mris_label2annot (you get to specify the color)

doug

On 02/26/2014 05:12 PM, Yang, Daniel wrote: Dear FreeSurfer experts,

Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color?

I want to show two labels, one is within the other one.

If yes, could you please tell me the specific steps..?

thanks a lot! Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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.

the other thing you could do is draw a path in tksurfer and have it be the "outline", then load the inner label and display it as filled On Wed, 26 Feb 2014, Douglas N Greve wrote:

No, you'd have to modify the label itself to exclude the center (and create an outline). I don't have any code to do this. For the other stuff, look at the help for mris_label2annot --help doug On 02/26/2014 05:35 PM, Yang, Daniel wrote:

...

Doug,

Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled?

I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case...

Best, Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_

On 2/26/14 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

I'm not sure about freeview, but you cannot do it in tksurfer. You
can
take your two labels and create an annotation with
mris_label2annot (you
get to specify the color)

doug

On 02/26/2014 05:12 PM, Yang, Daniel wrote:

    Dear FreeSurfer experts,

    Is it possible to display two labels in tksurfer or freeview,
    where
    one label is outlined with a certain color and the other label is
    filled with a different color?

    I want to show two labels, one is within the other one.

    If yes, could you please tell me the specific steps..?

    thanks a lot!
    Daniel

    --
    Daniel (Yung-Jui) Yang, Ph.D.
    Postdoctoral Researcher
    Yale Child Study Center
    New Haven, CT
    Tel: (203) 737-5454
    E-mail: _yung-jui.yang@yale.edu_ <mailto:_yung-jui.yang@yale.edu_>


    _______________________________________________
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    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 <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
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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
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dispose of the e-mail.

that's a good way to do it. You don't even need to save it as an mgz. You can just do tools->labels->copy label stats to overlay, then delete the label and you have an overlay from it (assuming the label->stat field is not zero) On Thu, 27 Feb 2014, Yang, Daniel wrote:

Thanks for both of you for the helps! I also find a 3rd solution: convert one of the labels to mgh and thus use it as overlay and use the other one as label in freeview.

Doug: Creating an outlined label sounds pretty cool. I wonder whether either erosion or dilution would do the trick … some sort of tricky conjunction.

Bruce: thanks!!

--  Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 2/26/14 5:52 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

  the other thing you could do is draw a path in tksurfer and have
  it be

the "outline", then load the inner label and display it as filled On Wed, 26 Feb 2014, Douglas N Greve wrote:

  No, you'd have to modify the label itself to exclude the
  center (and

create an outline). I don't have any code to do this. For the other stuff, look at the help for mris_label2annot --help doug On 02/26/2014 05:35 PM, Yang, Daniel wrote: Doug,

Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled?

I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case...

Best, Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_

On 2/26/14 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

I'm not sure about freeview, but you cannot do it in tksurfer. You      can      take your two labels and create an annotation with      mris_label2annot (you      get to specify the color)

doug

On 02/26/2014 05:12 PM, Yang, Daniel wrote:

Dear FreeSurfer experts,

Is it possible to display two labels in tksurfer or freeview,          where          one label is outlined with a certain color and the other label is          filled with a different color?

I want to show two labels, one is within the other one.

If yes, could you please tell me the specific steps..?

thanks a lot!          Daniel

--          Daniel (Yung-Jui) Yang, Ph.D.          Postdoctoral Researcher          Yale Child Study Center          New Haven, CT          Tel: (203) 737-5454          E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_

_______________________________________________          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 mailto:greve@nmr.mgh.harvard.edu      Phone Number: 617-724-2358      Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting      FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2      www.nmr.mgh.harvard.edu/facility/filedrop/index.html      Outgoing:      ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________      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.

By the way, what command can I use to erode a label/mgh..? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 2/26/14 7:03 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

that's a good way to do it. You don't even need to save it as an mgz. You can just do tools->labels->copy label stats to overlay, then delete the label and you have an overlay from it (assuming the label->stat field is not zero) On Thu, 27 Feb 2014, Yang, Daniel wrote:

Thanks for both of you for the helps! I also find a 3rd solution: convert one of the labels to mgh and thus use it as overlay and use the other one as label in freeview. Doug: Creating an outlined label sounds pretty cool. I wonder whether either erosion or dilution would do the trick … some sort of tricky conjunction. Bruce: thanks!! -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu On 2/26/14 5:52 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

the other thing you could do is draw a path in tksurfer and have it be the "outline", then load the inner label and display it as filled On Wed, 26 Feb 2014, Douglas N Greve wrote:

No, you'd have to modify the label itself to exclude the center (and create an outline). I don't have any code to do this. For the other stuff, look at the help for mris_label2annot --help doug On 02/26/2014 05:35 PM, Yang, Daniel wrote: Doug, Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled? I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case... Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 2/26/14 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote: I'm not sure about freeview, but you cannot do it in tksurfer. You can take your two labels and create an annotation with mris_label2annot (you get to specify the color) doug On 02/26/2014 05:12 PM, Yang, Daniel wrote: Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

Thanks, Bruce! I also found in tksurfer --> Tools --> Labels --> Erode/Dilate Selected Label !

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 2/26/14 8:02 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

mri_morphology for the .mgz

for the label you can do it in tksurfer in the tools->label menu or use mri_label2label (at least I put it in the dev version, not sure if it is released yet) On Thu, 27 Feb 2014, Yang, Daniel wrote:

By the way, what command can I use to erode a label/mgh..? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu On 2/26/14 7:03 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

that's a good way to do it. You don't even need to save it as an mgz. You can just do tools->labels->copy label stats to overlay, then delete the label and you have an overlay from it (assuming the label->stat field is not zero) On Thu, 27 Feb 2014, Yang, Daniel wrote:

Thanks for both of you for the helps! I also find a 3rd solution: convert one of the labels to mgh and thus use it as overlay and use the other one as label in freeview. Doug: Creating an outlined label sounds pretty cool. I wonder whether either erosion or dilution would do the trick … some sort of tricky conjunction. Bruce: thanks!! -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu On 2/26/14 5:52 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: the other thing you could do is draw a path in tksurfer and have it be the "outline", then load the inner label and display it as filled On Wed, 26 Feb 2014, Douglas N Greve wrote: No, you'd have to modify the label itself to exclude the center (and create an outline). I don't have any code to do this. For the other stuff, look at the help for mris_label2annot --help doug On 02/26/2014 05:35 PM, Yang, Daniel wrote: Doug, Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled? I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case... Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 2/26/14 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote: I'm not sure about freeview, but you cannot do it in tksurfer. You can take your two labels and create an annotation with mris_label2annot (you get to specify the color) doug On 02/26/2014 05:12 PM, Yang, Daniel wrote: Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.