Re: [Freesurfer] Colourful Brain

2019-04-02 Thread May, Markus 
Hi Mike,
That looks awesome! Thank you very much for your help, I can’t wait to test it.

Markus

> Am 02.04.2019 um 17:36 schrieb Angstadt, Mike :
> 
>External Email - Use Caution
> 
> I've also done a brain print in color using Shapeways. There are probably a 
> number of ways to do it, but what ended up working for me is up on my github 
> at https://github.com/mangstad/freesurfer_to_3dprint
> 
> This uses freesurfer utilities to output the mesh to a more usable format, 
> then creates per vertex color information from an annotation file and then 
> runs a few modifications/fixes (reducing number of faces and some other 
> stuff) and then outputs into an x3d file with color information.
> 
> A lot of trial an error was involved, and some things that should have worked 
> didn't seem to for some reason, either errors on how I was handling the 
> format or problems with getting Shapeways to recognize the format with color, 
> etc.
> 
> -Mike
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tim Schäfer 
> 
> Sent: Tuesday, April 2, 2019 10:37:21 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Colourful Brain
> 
> External Email - Use Caution
> 
>External Email - Use Caution
> 
> This depends on the 3D model formats that your 3D printer will accept, and of 
> course what you want the colors to be (e.g., it could be different brain 
> regions according to some atlas, or a colormap of some cortical measurement 
> like the curvature at that point of the brain surface).
> 
> Maybe there is an easier way that somebody else on this list knows, but I 
> have written an exporter that can write a FreeSurfer brain mesh and the 
> respective morphometry data to a vertex-colored PLY (Stanford format) mesh 
> file.
> 
> You could use it and then use standard modeling software like Blender to load 
> that format and export it to a variety of other formats. Maybe you will have 
> to reduce the mesh resolution in Blender before printing, or use a low-poly 
> version from the start for 3D printing (?). You will know better than me. ;)
> 
> Afaik there already is an easy way to convert the Freesurfer mesh files to 
> OBJ format, but I found no way to make it use vertex colors (which makes some 
> sense, since OBJ seems to have no official support for that).
> 
> If you are interested in the exporter, just let me know. It's open source. 
> You can see an example for a model with vertex colors that I exported to PLY 
> and then loaded into Blender here: https://vimeo.com/325645975
> 
> In that video, the color is rather uninteresting (it's the surface area at 
> each vertex), but you can see that it works.
> 
> Best,
> 
> Tim
> 
> 
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> 
>> On April 2, 2019 at 3:43 PM "May, Markus"  wrote:
>> 
>> 
>> Hi,
>> My university has a new FDM 3D printer which is able to print colours. They 
>> want to print a brain in colour or maybe in multiple colours.
>> Is there anybody who knows how I could get it?
>> 
>> Best,
>> Markus
>> 
>> 
>> With best regards,
>> M.Eng. Markus May
>> 
>> Ph.D. Student at
>> Technische Hochschule Mittelhessen - University of Applied Sciences
>> 
>> 
>> Wiesenstr. 14, 35390 Gießen, Germany
>> Gebäude D10, Raum 0.16
>> Telefon: 0049 641 309 2646
>> Mail: markus@lse.thm.de<mailto:markus@lse.thm.de>
>> Web: www.thm.de/imps<http://www.thm.de/imps><http://www.thm.de/imps>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
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> used for urgent or sensitive issues 
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Re: [Freesurfer] Colourful Brain

2019-04-02 Thread Angstadt, Mike 
External Email - Use Caution

I've also done a brain print in color using Shapeways. There are probably a 
number of ways to do it, but what ended up working for me is up on my github at 
https://github.com/mangstad/freesurfer_to_3dprint

This uses freesurfer utilities to output the mesh to a more usable format, then 
creates per vertex color information from an annotation file and then runs a 
few modifications/fixes (reducing number of faces and some other stuff) and 
then outputs into an x3d file with color information.

A lot of trial an error was involved, and some things that should have worked 
didn't seem to for some reason, either errors on how I was handling the format 
or problems with getting Shapeways to recognize the format with color, etc.

-Mike

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tim Schäfer 

Sent: Tuesday, April 2, 2019 10:37:21 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Colourful Brain

External Email - Use Caution

External Email - Use Caution

This depends on the 3D model formats that your 3D printer will accept, and of 
course what you want the colors to be (e.g., it could be different brain 
regions according to some atlas, or a colormap of some cortical measurement 
like the curvature at that point of the brain surface).

Maybe there is an easier way that somebody else on this list knows, but I have 
written an exporter that can write a FreeSurfer brain mesh and the respective 
morphometry data to a vertex-colored PLY (Stanford format) mesh file.

You could use it and then use standard modeling software like Blender to load 
that format and export it to a variety of other formats. Maybe you will have to 
reduce the mesh resolution in Blender before printing, or use a low-poly 
version from the start for 3D printing (?). You will know better than me. ;)

Afaik there already is an easy way to convert the Freesurfer mesh files to OBJ 
format, but I found no way to make it use vertex colors (which makes some 
sense, since OBJ seems to have no official support for that).

If you are interested in the exporter, just let me know. It's open source. You 
can see an example for a model with vertex colors that I exported to PLY and 
then loaded into Blender here: https://vimeo.com/325645975

In that video, the color is rather uninteresting (it's the surface area at each 
vertex), but you can see that it works.

Best,

Tim


--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

> On April 2, 2019 at 3:43 PM "May, Markus"  wrote:
>
>
> Hi,
> My university has a new FDM 3D printer which is able to print colours. They 
> want to print a brain in colour or maybe in multiple colours.
> Is there anybody who knows how I could get it?
>
> Best,
> Markus
> 
>
> With best regards,
> M.Eng. Markus May
>
> Ph.D. Student at
> Technische Hochschule Mittelhessen - University of Applied Sciences
>
>
> Wiesenstr. 14, 35390 Gießen, Germany
> Gebäude D10, Raum 0.16
> Telefon: 0049 641 309 2646
> Mail: markus@lse.thm.de<mailto:markus@lse.thm.de>
> Web: www.thm.de/imps<http://www.thm.de/imps><http://www.thm.de/imps>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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used for urgent or sensitive issues 



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Re: [Freesurfer] Colourful Brain

2019-04-02 Thread Tim Schäfer 
External Email - Use Caution

This depends on the 3D model formats that your 3D printer will accept, and of 
course what you want the colors to be (e.g., it could be different brain 
regions according to some atlas, or a colormap of some cortical measurement 
like the curvature at that point of the brain surface).

Maybe there is an easier way that somebody else on this list knows, but I have 
written an exporter that can write a FreeSurfer brain mesh and the respective 
morphometry data to a vertex-colored PLY (Stanford format) mesh file. 

You could use it and then use standard modeling software like Blender to load 
that format and export it to a variety of other formats. Maybe you will have to 
reduce the mesh resolution in Blender before printing, or use a low-poly 
version from the start for 3D printing (?). You will know better than me. ;)

Afaik there already is an easy way to convert the Freesurfer mesh files to OBJ 
format, but I found no way to make it use vertex colors (which makes some 
sense, since OBJ seems to have no official support for that).

If you are interested in the exporter, just let me know. It's open source. You 
can see an example for a model with vertex colors that I exported to PLY and 
then loaded into Blender here: https://vimeo.com/325645975

In that video, the color is rather uninteresting (it's the surface area at each 
vertex), but you can see that it works.

Best,

Tim


--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
 
> On April 2, 2019 at 3:43 PM "May, Markus"  wrote:
> 
> 
> Hi,
> My university has a new FDM 3D printer which is able to print colours. They 
> want to print a brain in colour or maybe in multiple colours.
> Is there anybody who knows how I could get it?
> 
> Best,
> Markus
> 
> 
> With best regards,
> M.Eng. Markus May
> 
> Ph.D. Student at
> Technische Hochschule Mittelhessen - University of Applied Sciences
> 
> 
> Wiesenstr. 14, 35390 Gießen, Germany
> Gebäude D10, Raum 0.16
> Telefon: 0049 641 309 2646
> Mail: markus@lse.thm.de
> Web: www.thm.de/imps
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Colourful Brain

2019-04-02 Thread May, Markus 
Hi,
My university has a new FDM 3D printer which is able to print colours. They 
want to print a brain in colour or maybe in multiple colours.
Is there anybody who knows how I could get it?

Best,
Markus


With best regards,
M.Eng. Markus May

Ph.D. Student at
Technische Hochschule Mittelhessen - University of Applied Sciences


Wiesenstr. 14, 35390 Gießen, Germany
Gebäude D10, Raum 0.16
Telefon: 0049 641 309 2646
Mail: markus@lse.thm.de
Web: www.thm.de/imps
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