Hello all,
I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this .
Regards Darshan
Hi Darshan
sorry, I don't think we do. YOu can convert to ascii or vtk or stl and see if you can go from there (using mris_convert)
cheers Bruce On Mon, 20 Feb 2012, Darshan P wrote:
Hello all,
I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this .
Regards Darshan
Hi Darshan,
as Bruce suggested, you can use mris_convert to get an STL file which you can import into Blender or MeshLab. Both write Wavefront OBJ files.
- Manfred
On 02/20/2012 07:24 PM, Darshan P wrote:
Hello all,
I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this .
Regards Darshan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
There's a how-to in the FreeSurfer website: http://surfer.nmr.mgh.harvard.edu/fswiki/HowTo/HowTo
Pedro Paulo Jr.
On Mon, Feb 20, 2012 at 23:32, Manfred G Kitzbichler < manfredg@nmr.mgh.harvard.edu> wrote:
Hi Darshan,
as Bruce suggested, you can use mris_convert to get an STL file which you can import into Blender or MeshLab. Both write Wavefront OBJ files.
- ManfredOn 02/20/2012 07:24 PM, Darshan P wrote:
Hello all,
I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this .
Regards Darshan
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Manfred G. Kitzbichlerhttps://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=1377, Research Fellow Harvard Medical School & Mass General Hospital Martinos Center for Biomedical Imaging 149 Thirteenth Street, Rm 10.018 Charlestown, MA 02129, USA
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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.
Hi Darshan,
If you'd like to go directly from FreeSurfer .asc to OBJ, the attached little script should do the trick...
Hope it helps!
All the best,
Anderson
On 21/02/12 16:59, Pedro Paulo de Magalhães Oliveira Junior wrote:
There's a how-to in the FreeSurfer website: http://surfer.nmr.mgh.harvard.edu/fswiki/HowTo/HowTo
Pedro Paulo Jr.
On Mon, Feb 20, 2012 at 23:32, Manfred G Kitzbichler <manfredg@nmr.mgh.harvard.edu mailto:manfredg@nmr.mgh.harvard.edu> wrote:
Hi Darshan, as Bruce suggested, you can use mris_convert to get an STL file which you can import into Blender or MeshLab. Both write Wavefront OBJ files. - Manfred On 02/20/2012 07:24 PM, Darshan P wrote:Hello all, I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this . Regards Darshan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Manfred G. Kitzbichler <https://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=1377>, Research Fellow Harvard Medical School & Mass General Hospital Martinos Center for Biomedical Imaging 149 Thirteenth Street, Rm 10.018 Charlestown, MA 02129, USA _______________________________________________ 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.
Hi Gabriel,
Once you have the surface in FS binary format (native format), the command to convert to surface ASCII I believe is mris_convert. Not sure if mri_convert will work as I think that is for volumes.
With the surface ASCII in hands, then run:
/ srf2obj surface.asc > surface.obj/
Note that the symbol ">" is needed to redirect the converted result to a new file.
Hope this helps!
All the best,
Anderson
On 03/05/12 10:16, Gabriel Gonzalez Escamilla wrote:
Dear Anderson, I have seen this message and I'm currently trying to use your script "srf2obj" to convert to obj format some surfaces created by FS, firstly i did convert the aseg into a volume in the native space using "mri_convert", after that, i'd transform the aseg volume into a surface mgh format (mri_vol2surf), then store the surface as ascii by using "mri_convert" then I'm using your script to convert that surface to an object file but always renturns the following error:
aplication srf2obj
gawk: /root/trabajo/freesurfer/bin/srf2obj:2: ' inválido en la expresiónrfer/bin/srf2obj:2: ^ caracter '
I'm working under centOS 4.3
Best Regards, Gabriel
El 22/02/12, *Anderson Winkler * andersonwinkler@hotmail.com escribió:
Hi Darshan,
If you'd like to go directly from FreeSurfer .asc to OBJ, the attached little script should do the trick...
Hope it helps!
All the best,
Anderson
On 21/02/12 16:59, Pedro Paulo de Magalhães Oliveira Junior wrote:
There's a how-to in the FreeSurfer website: http://surfer.nmr.mgh.harvard.edu/fswiki/HowTo/HowTo
Pedro Paulo Jr.
On Mon, Feb 20, 2012 at 23:32, Manfred G Kitzbichler <manfredg@nmr.mgh.harvard.edu manfredg@nmr.mgh.harvard.edu> wrote:
Hi Darshan, as Bruce suggested, you can use mris_convert to get an STL file which you can import into Blender or MeshLab. Both write Wavefront OBJ files. - Manfred On 02/20/2012 07:24 PM, Darshan P wrote:Hello all, I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this . Regards Darshan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Manfred G. Kitzbichler <https://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=1377>, Research Fellow Harvard Medical School & Mass General Hospital Martinos Center for Biomedical Imaging 149 Thirteenth Street, Rm 10.018 Charlestown, MA 02129, USA _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <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.eduFreesurfer@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.
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
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@nmr.mgh.harvard.edu
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Anderson Winkler -
Bruce Fischl -
Darshan P -
Gabriel Gonzalez Escamilla -
Manfred G Kitzbichler -
Pedro Paulo de Magalhães Oliveira Junior