ops, it seems the comments inside the dpxwrite.m no longer reflect what it does. You probably don't need this, but anyway, the version attached is more up-to-date. Anderson

On 08/10/11 17:28, Anderson Winkler wrote:

Hi Pedro,

There is probably a way to do that using FS tools from the command line, but the attached script should do the same. The result is a "data-per-vertex" file, which is the same as the .asc files from mris_convert. There is no geometry input, hence the vertex coordinates are all set to (0,0,0).

Hope it helps!

All the best,

Anderson

On 08/10/11 17:17, Pedro Paulo de Magalhães Oliveira Junior wrote:

...

I need to create a file where I have the parcellation value (structure name) per vertex.

I've tried mris_convert --annot /Applications/freesurfer/subjects/bert/label/lh.aparc.annot /Applications/freesurfer/subjects/bert/surf/lh.pial parc.asc

But I get the error: ERROR: unknown file annot file type specified for output: saida.asc

Has someone done this before?

Thanks

Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br http://www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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Thanks.

I suppose I can't do this without matlab. Right?

-- iOS 5.0

Em 08/10/2011, às 19:29, Bruce Fischl fischl@nmr.mgh.harvard.edu escreveu:

there is a write_annotation.m file you can use On Sat, 8 Oct 2011, Anderson Winkler wrote:

...

ops, it seems the comments inside the dpxwrite.m no longer reflect what it does. You probably don't need this, but anyway, the version attached is more up-to-date. Anderson On 08/10/11 17:28, Anderson Winkler wrote: Hi Pedro,

 There is probably a way to do that using FS tools from the command line, but the attached script should do the same. The result is a "data-per-vertex" file, which
 is the same as the .asc files from mris_convert. There is no geometry input, hence the vertex coordinates are all set to (0,0,0).

 Hope it helps!

 All the best,

 Anderson

 On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior wrote:
       I need to create a file where I have the parcellation value (structure name) per vertex.

I've tried�mris_convert --annot /Applications/freesurfer/subjects/bert/label/lh.aparc.annot /Applications/freesurfer/subjects/bert/surf/lh.pial parc.asc But I get the error:�ERROR: unknown file annot file type specified for output: saida.asc Has someone done this before? Thanks

---

Pedro Paulo de Magalh�es Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile:�http://itunes.apple.com/br/artist/netfilter/id365306441 _______________________________________________ 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. _______________________________________________ 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.

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If you know Python, you can likely do this pretty easily with tools from the PySurfer package: http://pysurfer.github.com/

(Check out surfer.io.read_annotation).

If you're just using the io routines, you won't need the somewhat heavy Mayavi visualization dependencies. You should be able to read in and manipulate surfaces/annotations just with numpy.

Best, Michael

2011/10/8 Bruce Fischl fischl@nmr.mgh.harvard.edu

it wouldn't be that hard to put something together if you want to avoid matlab. Spec out what you need and send me a sample, maybe on Bert

Bruce

On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:

Thanks.

...

I suppose I can't do this without matlab. Right?

-- iOS 5.0

Em 08/10/2011, às 19:29, Bruce Fischl fischl@nmr.mgh.harvard.edu escreveu:

there is a write_annotation.m file you can use

...

On Sat, 8 Oct 2011, Anderson Winkler wrote:

ops, it seems the comments inside the dpxwrite.m no longer reflect what

...

it does. You probably don't need this, but anyway, the version attached is more up-to-date. Anderson On 08/10/11 17:28, Anderson Winkler wrote: Hi Pedro,

There is probably a way to do that using FS tools from the command

line, but the attached script should do the same. The result is a "data-per-vertex" file, which is the same as the .asc files from mris_convert. There is no geometry input, hence the vertex coordinates are all set to (0,0,0).

Hope it helps!

All the best,

Anderson

On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior wrote:
      I need to create a file where I have the parcellation value

(structure name) per vertex. I've tried�mris_convert --annot /Applications/freesurfer/** subjects/bert/label/lh.aparc.**annot /Applications/freesurfer/**subjects/bert/surf/lh.pial parc.asc But I get the error:�ERROR: unknown file annot file type specified for output: saida.asc Has someone done this before? Thanks

------------------------------**------------------------------**

Pedro Paulo de Magalh�es Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile:�http://itunes.apple.**com/br/artist/netfilter/** id365306441 http://itunes.apple.com/br/artist/netfilter/id365306441 ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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. ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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.

______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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.

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Have you tried using mri_annotation2label with the --seg output option? doug

Michael Waskom wrote:

If you know Python, you can likely do this pretty easily with tools from the PySurfer package: http://pysurfer.github.com/

(Check out surfer.io.read_annotation).

If you're just using the io routines, you won't need the somewhat heavy Mayavi visualization dependencies. You should be able to read in and manipulate surfaces/annotations just with numpy.

Best, Michael

2011/10/8 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>

it wouldn't be that hard to put something together if you want to
avoid matlab. Spec out what you need and send me a sample, maybe
on Bert

Bruce

On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:

    Thanks.

    I suppose I can't do this without matlab. Right?

    -- iOS 5.0

    Em 08/10/2011, às 19:29, Bruce Fischl
    <fischl@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>> escreveu:

        there is a write_annotation.m file you can use
        On Sat, 8 Oct 2011, Anderson Winkler wrote:

            ops, it seems the comments inside the dpxwrite.m no
            longer reflect what it does. You probably don't need
            this, but anyway, the version attached is more up-to-date.
            Anderson
            On 08/10/11 17:28, Anderson Winkler wrote:
                Hi Pedro,

                There is probably a way to do that using FS tools
            from the command line, but the attached script should
            do the same. The result is a "data-per-vertex" file, which
                is the same as the .asc files from mris_convert.
            There is no geometry input, hence the vertex
            coordinates are all set to (0,0,0).

                Hope it helps!

                All the best,

                Anderson

                On 08/10/11 17:17, Pedro Paulo de Magalh�es
            Oliveira Junior wrote:
                      I need to create a file where I have the
            parcellation value (structure name) per vertex.
            I've tried�mris_convert --annot
            /Applications/freesurfer/
            subjects/bert/label/lh.aparc. annot
            /Applications/freesurfer/ subjects/bert/surf/lh.pial
            parc.asc
            But I get the error:�ERROR: unknown file annot file
            type specified for output: saida.asc
            Has someone done this before?
            Thanks
            ------------------------------
            ------------------------------ ---------
            Pedro Paulo de Magalh�es Oliveira Junior
            Netfilter & SpeedComm Telecom -- www.netfilter.com.br
            <http://www.netfilter.com.br>
            -- For mobile:�http://itunes.apple.
            com/br/artist/netfilter/ id365306441
            <http://itunes.apple.com/br/artist/netfilter/id365306441>
            ______________________________ _________________
            Freesurfer mailing list
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            freesurfer
            <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Michael,

Thanks for the hint.

Here's a program that converts the surface + annotation in a Stanford PLY Object file

# Create ply # Stanford Object format from surfer import io as io_

surface = io_.read_geometry ('/Applications/freesurfer/subjects/bert/surf/lh.pial') labels = io_.read_annot ('/Applications/freesurfer/subjects/bert/label/lh.aparc.annot')

facenum = len(surface[1]) vertnum = len(surface[0])

print "ply" print "format ascii 1.0" print "comment VCGLIB generated" print "element vertex %d"%vertnum print "property float x" print "property float y" print "property float z" #print "property int flags" print "property uchar red" print "property uchar green" print "property uchar blue" print "property uchar alpha" print "element face %d"%facenum print "property list uchar int vertex_indices" print "end_header" for i in xrange(vertnum): vert = surface[0][i]; color = labels[1][labels[0][i]] print "%f %f %f %d %d %d %d"%(vert[0],vert[1],vert[2],color[0],color[1],color[2],color[3])

for i in xrange(facenum): face = surface[1][i] print "3 %d %d %d"%(face[0],face[1],face[2])

2011/10/9 Michael Waskom mwaskom@stanford.edu

If you know Python, you can likely do this pretty easily with tools from the PySurfer package: http://pysurfer.github.com/

(Check out surfer.io.read_annotation).

If you're just using the io routines, you won't need the somewhat heavy Mayavi visualization dependencies. You should be able to read in and manipulate surfaces/annotations just with numpy.

Best, Michael

2011/10/8 Bruce Fischl fischl@nmr.mgh.harvard.edu

...

it wouldn't be that hard to put something together if you want to avoid matlab. Spec out what you need and send me a sample, maybe on Bert

Bruce

On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:

Thanks.

...

I suppose I can't do this without matlab. Right?

-- iOS 5.0

Em 08/10/2011, às 19:29, Bruce Fischl fischl@nmr.mgh.harvard.edu escreveu:

there is a write_annotation.m file you can use

...

On Sat, 8 Oct 2011, Anderson Winkler wrote:

ops, it seems the comments inside the dpxwrite.m no longer reflect what

...

it does. You probably don't need this, but anyway, the version attached is more up-to-date. Anderson On 08/10/11 17:28, Anderson Winkler wrote: Hi Pedro,

There is probably a way to do that using FS tools from the command

line, but the attached script should do the same. The result is a "data-per-vertex" file, which is the same as the .asc files from mris_convert. There is no geometry input, hence the vertex coordinates are all set to (0,0,0).

Hope it helps!

All the best,

Anderson

On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior

wrote: I need to create a file where I have the parcellation value (structure name) per vertex. I've tried�mris_convert --annot /Applications/freesurfer/** subjects/bert/label/lh.aparc.**annot /Applications/freesurfer/**subjects/bert/surf/lh.pial parc.asc But I get the error:�ERROR: unknown file annot file type specified for output: saida.asc Has someone done this before? Thanks

------------------------------**------------------------------**

Pedro Paulo de Magalh�es Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile:�http://itunes.apple.**com/br/artist/netfilter/** id365306441 http://itunes.apple.com/br/artist/netfilter/id365306441 ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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. ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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.

______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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.

---

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oops, sorry list, this was supposed to go to Pedro...

On 15/10/11 17:39, Anderson Winkler wrote:

Ah Pedro, Se era isso que você precisava, poderia ter falado. Eu tenho isso pronto, que pode ser chamado via linha de comandos. Foi usado no paper que vc deve ter visto... Abração, Anderson

On 15/10/11 13:09, Pedro Paulo de Magalhães Oliveira Junior wrote:

...

Michael,

Thanks for the hint.

Here's a program that converts the surface + annotation in a Stanford PLY Object file

# Create ply # Stanford Object format from surfer import io as io_

surface = io_.read_geometry ('/Applications/freesurfer/subjects/bert/surf/lh.pial') labels = io_.read_annot ('/Applications/freesurfer/subjects/bert/label/lh.aparc.annot')

facenum = len(surface[1]) vertnum = len(surface[0])

print "ply" print "format ascii 1.0" print "comment VCGLIB generated" print "element vertex %d"%vertnum print "property float x" print "property float y" print "property float z" #print "property int flags" print "property uchar red" print "property uchar green" print "property uchar blue" print "property uchar alpha" print "element face %d"%facenum print "property list uchar int vertex_indices" print "end_header" for i in xrange(vertnum): vert = surface[0][i]; color = labels[1][labels[0][i]] print "%f %f %f %d %d %d %d"%(vert[0],vert[1],vert[2],color[0],color[1],color[2],color[3])

for i in xrange(facenum): face = surface[1][i] print "3 %d %d %d"%(face[0],face[1],face[2])

2011/10/9 Michael Waskom <mwaskom@stanford.edu mailto:mwaskom@stanford.edu>

If you know Python, you can likely do this pretty easily with
tools from the PySurfer package: http://pysurfer.github.com/

(Check out surfer.io.read_annotation).

If you're just using the io routines, you won't need the somewhat
heavy Mayavi visualization dependencies.  You should be able to
read in and manipulate surfaces/annotations just with numpy.

Best,
Michael


2011/10/8 Bruce Fischl <fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>

    it wouldn't be that hard to put something together if you
    want to avoid matlab. Spec out what you need and send me a
    sample, maybe on Bert

    Bruce

    On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior
    wrote:

        Thanks.

        I suppose I can't do this without matlab. Right?

        -- iOS 5.0

        Em 08/10/2011, às 19:29, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu
        <mailto:fischl@nmr.mgh.harvard.edu>> escreveu:

            there is a write_annotation.m file you can use
            On Sat, 8 Oct 2011, Anderson Winkler wrote:

                ops, it seems the comments inside the dpxwrite.m
                no longer reflect what it does. You probably
                don't need this, but anyway, the version attached
                is more up-to-date.
                Anderson
                On 08/10/11 17:28, Anderson Winkler wrote:
                    Hi Pedro,

                    There is probably a way to do that using FS
                tools from the command line, but the attached
                script should do the same. The result is a
                "data-per-vertex" file, which
                    is the same as the .asc files from
                mris_convert. There is no geometry input, hence
                the vertex coordinates are all set to (0,0,0).

                    Hope it helps!

                    All the best,

                    Anderson

                    On 08/10/11 17:17, Pedro Paulo de Magalh�es
                Oliveira Junior wrote:
                          I need to create a file where I have
                the parcellation value (structure name) per vertex.
                I've tried�mris_convert --annot
                /Applications/freesurfer/subjects/bert/label/lh.aparc.annot
                /Applications/freesurfer/subjects/bert/surf/lh.pial
                parc.asc
                But I get the error:�ERROR: unknown file annot
                file type specified for output: saida.asc
                Has someone done this before?
                Thanks
                ---------------------------------------------------------------------
                Pedro Paulo de Magalh�es Oliveira Junior
                Netfilter & SpeedComm Telecom --
                www.netfilter.com.br <http://www.netfilter.com.br>
                -- For
                mobile:�http://itunes.apple.com/br/artist/netfilter/id365306441
                _______________________________________________
                Freesurfer mailing list
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                <mailto:Freesurfer@nmr.mgh.harvard.edu>
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                The information in this e-mail is intended only
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                you in error and the e-mail
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                http://www.partners.org/complianceline . If the
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                but does not contain patient information, please
                contact the sender and properly
                dispose of the e-mail.
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                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.

            _______________________________________________
            Freesurfer mailing list
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            <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.




    _______________________________________________
    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.

---

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.

---

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.