Hi Bruce,

So when I'm at this page, I am separating the different parts of the brain so that in the 3D view they show up as their own entity, and I am trying to individually save them. When I press the save button shown on the left hand side of the screen, it saves as a .vtk file, which makes it difficult to upload into matlab. Is there a way to convert this 3D brain piece as an .mgz file?

Thanks

On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

What segmentation do you mean? Where are you getting vtk files? We write the segmentation into .mgz volumes such as aseg.mgz

Cheers Bruce

On Jul 18, 2016, at 1:19 PM, Abbie McNulty amcnult1@stanford.edu wrote:

So we were able to figure out how to segment the different parts of the brain using the bert sample, but have run into another problem. I would like to save each segmentation so that I can import it into matlab and create a matrix in order to create a mesh. The volume segment saves a as a .vtk file, which I don't know how to read into matlab. How can I save it as or convert it to a .mgz file so that I can import it into matlab?

Thanks!

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I attached the page in the last message, maybe it didn't show. I guess they aren't called segmentations, but isolation. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithD... This link describes the process that am I am working with, and there is an option to save these isolated pieces, and they save as a .vtk file, I am not converting anything

Abbie

On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Abbie

I'm not sure what page you mean. The segmentations start life as an .mgz file, so why convert them at all? Just load the aseg.mgz (or whichever segmentation you are interested in) into matlab directly

cheers Bruce

On Tue, 19 Jul 2016, Abbie McNulty wrote:

Hi Bruce,

...

So when I'm at this page, I am separating the different parts of the brain so that in the 3D view they show up as their own entity, and I am trying to individually save them. When I press the save button shown on the left hand side of the screen, it saves as a .vtk file, which makes it difficult to upload into matlab. Is there a way to convert this 3D brain piece as an .mgz file?

Thanks

On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: What segmentation do you mean? Where are you getting vtk files? We write the segmentation into .mgz volumes such as aseg.mgz

Cheers Bruce

On Jul 18, 2016, at 1:19 PM, Abbie McNulty amcnult1@stanford.edu wrote:

  So we were able to figure out how to segment the different parts of

the brain using the bert sample, but have run into another problem. I would like to save each segmentation so that I can import it into matlab and create a matrix in order to create a mesh. The volume segment saves a as a .vtk file, which I don't know how to read into matlab. How can I save it as or convert it to a .mgz file so that I can import it into matlab?

Thanks!

  _______________________________________________
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So say I load aseg.mgz into matlab and I want to extract the brainstem in matlab to plot its own volumetric mesh vs. the entire brain, how would I extract the brainstem in matlab?

On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

but why not just load the aseg.mgz or whatever volume you are using directly into matlab? Then each structure has a different index that you can extract with the find command

cheers Bruce On Tue, 19 Jul 2016, Abbie McNulty wrote:

I attached the page in the last message, maybe it didn't show. I guess

...

they aren't called segmentations, but isolation. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithD... This link describes the process that am I am working with, and there is an option to save these isolated pieces, and they save as a .vtk file, I am not converting anything

Abbie

On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Abbie

  I'm not sure what page you mean. The segmentations start life as an

.mgz file, so why convert them at all? Just load the aseg.mgz (or whichever segmentation you are interested in) into matlab directly

  cheers
  Bruce


  On Tue, 19 Jul 2016, Abbie McNulty wrote:

        Hi Bruce,
        So when I'm at this page, I am separating the different parts

of the brain so that in the 3D view they show up as their own entity, and I am trying to individually save them. When I press the save button shown on the left hand side of the screen, it saves as a .vtk file, which makes it difficult to upload into matlab. Is there a way to convert this 3D brain piece as an .mgz file?

        Thanks

        On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl <

fischl@nmr.mgh.harvard.edu> wrote: What segmentation do you mean? Where are you getting vtk files? We write the segmentation into .mgz volumes such as aseg.mgz

        Cheers
        Bruce


        On Jul 18, 2016, at 1:19 PM, Abbie McNulty <

amcnult1@stanford.edu> wrote:

              So we were able to figure out how to segment the

different parts of the brain using the bert sample, but have run into another problem. I would like to save each segmentation so that I can import it into matlab and create a matrix in order to create a mesh. The volume segment saves a as a .vtk file, which I don't know how to read into matlab. How can I save it as or convert it to a .mgz file so that I can import it into matlab?

        Thanks!

              _______________________________________________
              Freesurfer mailing list
              Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

        _______________________________________________
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        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.

        --
        Abigail C. McNulty
        Stanford University Class of 2018
        B.A. Candidate in Bioengineering
        Stanford Women's XC/ Track and Field

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-- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field

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Perfect. now if I wanted to use plotmesh with this, what would the variables be for x and y: plotmesh('x,y')

On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

[aseg,M,mr] = load_mgh('aseg.mgz'); ind = find(aseg == 16);

that will give you the indices in the aseg volume of the voxels that have the brainstem label (16). Then you can do what you want with it. The label came from $FREESURFER_HOME/FreeSurferColorLUT.txt

cheers Bruce

On Tue, 19 Jul 2016, Abbie McNulty wrote:

So say I load aseg.mgz into matlab and I want to extract the brainstem in

...

matlab to plot its own volumetric mesh vs. the entire brain, how would I extract the brainstem in matlab?

On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: but why not just load the aseg.mgz or whatever volume you are using directly into matlab? Then each structure has a different index that you can extract with the find command

  cheers
  Bruce
  On Tue, 19 Jul 2016, Abbie McNulty wrote:

        I attached the page in the last message, maybe it didn't

show. I guess they aren't called segmentations, but isolation. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithD... This link describes the process that am I am working with, and there is an option to save these isolated pieces, and they save as a .vtk file, I am not converting anything

        Abbie

        On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl <

fischl@nmr.mgh.harvard.edu> wrote: Hi Abbie

              I'm not sure what page you mean. The segmentations

start life as an .mgz file, so why convert them at all? Just load the aseg.mgz (or whichever segmentation you are interested in) into matlab directly

              cheers
              Bruce


              On Tue, 19 Jul 2016, Abbie McNulty wrote:

                    Hi Bruce,
                    So when I'm at this page, I am separating the

different parts of the brain so that in the 3D view they show up as their own entity, and I am trying to individually save them. When I press the save button shown on the left hand side of the screen, it saves as a .vtk file, which makes it difficult to upload into matlab. Is there a way to convert this 3D brain piece as an .mgz file?

                    Thanks

                    On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl <

fischl@nmr.mgh.harvard.edu> wrote: What segmentation do you mean? Where are you getting vtk files? We write the segmentation into .mgz volumes such as aseg.mgz

                    Cheers
                    Bruce


                    On Jul 18, 2016, at 1:19 PM, Abbie McNulty <

amcnult1@stanford.edu> wrote:

                          So we were able to figure out how to

segment the different parts of the brain using the bert sample, but have run into another problem. I would like to save each segmentation so that I can import it into matlab and create a matrix in order to create a mesh. The volume segment saves a as a .vtk file, which I don't know how to read into matlab. How can I save it as or convert it to a .mgz file so that I can import it into matlab?

                    Thanks!

---

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                          Freesurfer@nmr.mgh.harvard.edu

https://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.

                    --
                    Abigail C. McNulty
                    Stanford University Class of 2018
                    B.A. Candidate in Bioengineering
                    Stanford Women's XC/ Track and Field


        _______________________________________________
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        Freesurfer@nmr.mgh.harvard.edu
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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.

        --
        Abigail C. McNulty
        Stanford University Class of 2018
        B.A. Candidate in Bioengineering
        Stanford Women's XC/ Track and Field

---

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-- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field

---

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sorry, perhaps someone else can help you with this. I haven't used plotmesh.

cheers Bruce On Tue, 19 Jul 2016, Abbie McNulty wrote:

Perfect. now if I wanted to use plotmesh with this, what would the variables be for x and y: plotmesh('x,y')

On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

  [aseg,M,mr] = load_mgh('aseg.mgz');
  ind = find(aseg == 16);


  that will give you the indices in the aseg volume of the voxels
  that have the brainstem label (16). Then you can do what you
  want with it. The label came from
  $FREESURFER_HOME/FreeSurferColorLUT.txt

  cheers
  Bruce

  On Tue, 19 Jul 2016, Abbie McNulty wrote:

        So say I load aseg.mgz into matlab and I want to
        extract the brainstem in matlab to plot its own
        volumetric mesh vs. the entire brain, how would I
        extract
        the brainstem in matlab?

        On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu> wrote:
              but why not just load the aseg.mgz or whatever
        volume you are using directly into matlab? Then each
        structure has a different index that you can
              extract with the find command

              cheers
              Bruce
              On Tue, 19 Jul 2016, Abbie McNulty wrote:

                    I attached the page in the last message,
        maybe it didn't show. I guess they aren't called
        segmentations, but
                   isolation. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/Freeview
        WorkingWithData/FreeviewAnatomicalVolumes
                    This link describes the process that am
        I am working with, and there is an option to save
        these isolated pieces, and they save as a
                    .vtk file, I am not
                    converting anything

                    Abbie 

                    On Tue, Jul 19, 2016 at 10:51 AM, Bruce
        Fischl <fischl@nmr.mgh.harvard.edu> wrote:
                          Hi Abbie

                          I'm not sure what page you mean.
        The segmentations start life as an .mgz file, so why
        convert them at all? Just load the
                    aseg.mgz (or whichever
                          segmentation you are interested
        in) into matlab directly

                          cheers
                          Bruce


                          On Tue, 19 Jul 2016, Abbie McNulty
        wrote:

                                Hi Bruce,
                                So when I'm at this page, I
        am separating the different parts of the brain so
        that in the 3D view they show up as their
                    own entity,
                                and I am trying to
                                individually save them. When
        I press the save button shown on the left hand side
        of the screen, it saves as a .vtk file,
                    which makes
                                it difficult to upload
                                into matlab. Is there a way
        to convert this 3D brain piece as an .mgz file?

                                Thanks

                                On Mon, Jul 18, 2016 at 5:40
        PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
                                What segmentation do you
        mean? Where are you getting vtk files? We write the
        segmentation into .mgz volumes such as
                    aseg.mgz


                                Cheers
                                Bruce


                                On Jul 18, 2016, at 1:19 PM,
        Abbie McNulty <amcnult1@stanford.edu> wrote:

                                      So we were able to
        figure out how to segment the different parts of the
        brain using the bert sample, but have run
                    into another
                                problem. 
                                I would like to save each
        segmentation so that I can import it into matlab and
        create a matrix in order to create a mesh.
                    The volume
                                segment
                                saves a as a .vtk file,
        which I don't know how to read into matlab. How can
        I save it as or convert it to a .mgz file so
                    that I can
                                import it
                                into matlab?

                                Thanks!

                                     
        _______________________________________________
                                      Freesurfer mailing
        list
                                     
        Freesurfer@nmr.mgh.harvard.edu
                                     
        https://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.




                                --
                                Abigail C. McNulty
                                Stanford University Class of
        2018
                                B.A. Candidate in
        Bioengineering
                                Stanford Women's XC/ Track
        and Field


                   
        _______________________________________________
                    Freesurfer mailing list
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        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.




                    --
                    Abigail C. McNulty
                    Stanford University Class of 2018
                    B.A. Candidate in Bioengineering
                    Stanford Women's XC/ Track and Field


        _______________________________________________
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        The information in this e-mail is intended only for
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        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.




        --
        Abigail C. McNulty
        Stanford University Class of 2018
        B.A. Candidate in Bioengineering
        Stanford Women's XC/ Track and Field

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-- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field