3D Brain Models - Revision history

Chris: /* Free Surfer */

2019-05-29T16:32:25Z

Free Surfer

← Older revision		Revision as of 12:32, 29 May 2019
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	=Free Surfer=		=Free Surfer=
			The FreeSurfer surface meshes will be found in a participant's /surf directory. The surface meshes that look most like what you're probably thinking of are the .pial surface files, of which there are two: lh.pial and rh.pial. These will be the files we are working from for this process.

	==Create a WaveFront OBJ File==		==Create a WaveFront OBJ File==
	Use mris_convert to convert from FreeSurfer binary to ASCII:		Use mris_convert to convert from FreeSurfer binary to ASCII:

Chris: /* Scale */

2019-05-29T16:22:15Z

Scale

← Older revision		Revision as of 12:22, 29 May 2019
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	==Scale==		==Scale==
	Blender uses arbitrary ''Blender Units'' to describe the size of modeled objects. The units aren't important for animation, but are quite relevant when the objects represent something in the physical world. I don't want to recreate the instructions for changing scale n blender, but will instead point you to [https://daler.github.io/blender-for-3d-printing/interface/transforms.html a link]		Blender uses arbitrary ''Blender Units'' to describe the size of modeled objects. The units aren't important for animation, but are quite relevant when the objects represent something in the physical world. I don't want to recreate the instructions for changing scale in blender, but will instead point you to [https://daler.github.io/blender-for-3d-printing/interface/transforms.html a link].

	You will need to change the units to something meaningful (I prefer Metric), and you will find that after conversion, the brains will be absurdly large. I mean, like the brain will have the footprint of a small city block. I found that changing the units to metric, and then setting the scale to 0.001 (1 square equals .001m, or 1mm) and then scaling the object to 0.3 in the X,Y and Z axes yields brains that fit in a 4x4x5cm bounding box which is a reasonable desk trinket size.		You will need to change the units to something meaningful (I prefer Metric), and you will find that after conversion, the brains will be absurdly large. I mean, like the brain will have the footprint of a small city block. I found that changing the units to metric, and then setting the scale to 0.001 (1 square equals .001m, or 1mm) and then scaling the object to 0.3 in the X,Y and Z axes yields brains that fit in a 4x4x5cm bounding box which is a reasonable desk trinket size.

Chris: /* Blender */

2019-05-29T16:20:59Z

Blender

← Older revision		Revision as of 12:20, 29 May 2019
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	=Blender=		=Blender=
	Blender is a free 3D modeling and animation software package available for Windows, Mac and Linux. You can download it [[http://www.blender.org \| here]]. It has loads of features that will be meaningless to anyone without formal training in computer animation, but it has two features that are useful to this project: 1) it's free, and 2) it can import/export and manipulate 3D mesh files saved in different formats.		Blender is a free 3D modeling and animation software package available for Windows, Mac and Linux. You can download it [http://www.blender.org here]. It has loads of features that will be meaningless to anyone without formal training in computer animation, but it has two features that are useful to this project: 1) it's free, and 2) it can import/export and manipulate 3D mesh files saved in different formats.

	==Import==		==Import==
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	==Scale==		==Scale==
	Blender uses arbitrary ''Blender Units'' to describe the size of modeled objects. The units aren't important for animation, but are quite relevant when the objects represent something in the physical world. I don't want to recreate the instructions for changing scale n blender, but will instead point you to [[https://daler.github.io/blender-for-3d-printing/interface/transforms.html \| a link]]		Blender uses arbitrary ''Blender Units'' to describe the size of modeled objects. The units aren't important for animation, but are quite relevant when the objects represent something in the physical world. I don't want to recreate the instructions for changing scale n blender, but will instead point you to [https://daler.github.io/blender-for-3d-printing/interface/transforms.html a link]
	You will need to change the units to something meaningful (I prefer Metric), and you will find that after conversion, the brains will be absurdly large. I mean, like the brain will have the footprint of a small city block. I found that changing the units to metric, and then setting the scale to 0.001 (1 square equals .001m, or 1mm) and then scaling the object to 0.3 in the X,Y and Z axes yields brains that fit in a 4x4x5cm bounding box which is a reasonable desk trinket size.		You will need to change the units to something meaningful (I prefer Metric), and you will find that after conversion, the brains will be absurdly large. I mean, like the brain will have the footprint of a small city block. I found that changing the units to metric, and then setting the scale to 0.001 (1 square equals .001m, or 1mm) and then scaling the object to 0.3 in the X,Y and Z axes yields brains that fit in a 4x4x5cm bounding box which is a reasonable desk trinket size.

Chris: /* Use srf2obj to create a Blender-Compatible File */

2019-05-29T16:20:21Z

Use srf2obj to create a Blender-Compatible File

← Older revision		Revision as of 12:20, 29 May 2019
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	The srf2obj script requires the installation of gawk if it's not already installed. The script can be found in the '''scripts/Shell''' folder on ubfs, and should be in your path (copy it to your ~/bin directory if you don't already have it).		The srf2obj script requires the installation of gawk if it's not already installed. The script can be found in the '''scripts/Shell''' folder on ubfs, and should be in your path (copy it to your ~/bin directory if you don't already have it).
	srf2obj lh.pial.srf > lh.pial.obj		srf2obj lh.pial.srf > lh.pial.obj

			Repeat for both hemispheres.

	If you are reading this wiki and aren't part of my lab, here is the srf2obj gawk script. I stole it from Anderson WInkler's blog. The only change I made is that gawk is installed in /usr/bin/ on my distribution of Ubuntu. You can copy/paste the script below to a text file to make a script (you'll still have to make it executable).		If you are reading this wiki and aren't part of my lab, here is the srf2obj gawk script. I stole it from Anderson WInkler's blog. The only change I made is that gawk is installed in /usr/bin/ on my distribution of Ubuntu. You can copy/paste the script below to a text file to make a script (you'll still have to make it executable).

Chris: /* 3D Printing */

2019-05-29T16:18:34Z

3D Printing

← Older revision		Revision as of 12:18, 29 May 2019
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	=3D Printing=		=3D Printing=
	The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files. Before printing you will need to fix your STL files using the [[https://service.netfabb.com/login.php Netfabb online service]]. This web-based utility requires a free autodesk account, but after you go through the registration process, you will be able to log in and upload your STL brain file. After a short upload and processing period (a couple of minutes), the website will tell you the file has been processed and provide you with a download link. The file will have the label "_fixed" added to it, so you can easily tell which of your brain files have been checked to ensure printability.		The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files. Before printing you will need to fix your STL files using the [https://service.netfabb.com/login.php Netfabb online service]. This web-based utility requires a free autodesk account, but after you go through the registration process, you will be able to log in and upload your STL brain file. After a short upload and processing period (a couple of minutes), the website will tell you the file has been processed and provide you with a download link. The file will have the label "_fixed" added to it, so you can easily tell which of your brain files have been checked to ensure printability.

	If you are printing at UB, there is a form you can complete at [http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html this link].		If you are printing at UB, there is a form you can complete at [http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html this link].

	If you do not have access to UB's printing facility, there are many web-based companies that will print and mail you 3D prints of files you upload, such as [http://www.shapeways.com Shapeways] and [http://www.sculteo.com Sculpteo] (which I have personally used).		If you do not have access to UB's printing facility, there are many web-based companies that will print and mail you 3D prints of files you upload, such as [http://www.shapeways.com Shapeways] and [http://www.sculteo.com Sculpteo] (which I have personally used).

Chris: /* 3D Printing */

2019-05-29T16:18:14Z

3D Printing

← Older revision		Revision as of 12:18, 29 May 2019
Line 66:		Line 66:
	The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files. Before printing you will need to fix your STL files using the [[https://service.netfabb.com/login.php Netfabb online service]]. This web-based utility requires a free autodesk account, but after you go through the registration process, you will be able to log in and upload your STL brain file. After a short upload and processing period (a couple of minutes), the website will tell you the file has been processed and provide you with a download link. The file will have the label "_fixed" added to it, so you can easily tell which of your brain files have been checked to ensure printability.		The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files. Before printing you will need to fix your STL files using the [[https://service.netfabb.com/login.php Netfabb online service]]. This web-based utility requires a free autodesk account, but after you go through the registration process, you will be able to log in and upload your STL brain file. After a short upload and processing period (a couple of minutes), the website will tell you the file has been processed and provide you with a download link. The file will have the label "_fixed" added to it, so you can easily tell which of your brain files have been checked to ensure printability.

	If you are printing at UB, there is a form you can complete at [[http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html this link]].		If you are printing at UB, there is a form you can complete at [http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html this link].

	If you do not have access to UB's printing facility, there are many web-based companies that will print and mail you 3D prints of files you upload, such as [[http://www.shapeways.com Shapeways]] and [[http://www.sculteo.com Sculpteo]] (which I have personally used).		If you do not have access to UB's printing facility, there are many web-based companies that will print and mail you 3D prints of files you upload, such as [http://www.shapeways.com Shapeways] and [http://www.sculteo.com Sculpteo] (which I have personally used).

Chris: /* 3D Printing */

2019-05-29T16:17:28Z

3D Printing

← Older revision		Revision as of 12:17, 29 May 2019
Line 66:		Line 66:
	The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files. Before printing you will need to fix your STL files using the [[https://service.netfabb.com/login.php Netfabb online service]]. This web-based utility requires a free autodesk account, but after you go through the registration process, you will be able to log in and upload your STL brain file. After a short upload and processing period (a couple of minutes), the website will tell you the file has been processed and provide you with a download link. The file will have the label "_fixed" added to it, so you can easily tell which of your brain files have been checked to ensure printability.		The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files. Before printing you will need to fix your STL files using the [[https://service.netfabb.com/login.php Netfabb online service]]. This web-based utility requires a free autodesk account, but after you go through the registration process, you will be able to log in and upload your STL brain file. After a short upload and processing period (a couple of minutes), the website will tell you the file has been processed and provide you with a download link. The file will have the label "_fixed" added to it, so you can easily tell which of your brain files have been checked to ensure printability.

	If you are printing at UB, there is a form you can complete at [[http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html \| this link]].		If you are printing at UB, there is a form you can complete at [[http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html this link]].

	If you do not have access to UB's printing facility, there are many web-based companies that will print and mail you 3D prints of files you upload, such as [[http://www.shapeways.com \| Shapeways]] and [[http://www.sculteo.com \| Sculpteo]] (which I have personally used).		If you do not have access to UB's printing facility, there are many web-based companies that will print and mail you 3D prints of files you upload, such as [[http://www.shapeways.com Shapeways]] and [[http://www.sculteo.com Sculpteo]] (which I have personally used).

Chris: /* 3D Printing */

2019-05-29T16:17:04Z

3D Printing

← Older revision		Revision as of 12:17, 29 May 2019
Line 64:		Line 64:

	=3D Printing=		=3D Printing=
	The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files. Before printing you will need to fix your STL files using the [[https://service.netfabb.com/login.php \| Netfabb online service]]. This web-based utility requires a free autodesk account, but after you go through the registration process, you will be able to log in and upload your STL brain file. After a short upload and processing period (a couple of minutes), the website will tell you the file has been processed and provide you with a download link. The file will have the label "_fixed" added to it, so you can easily tell which of your brain files have been checked to ensure printability.		The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files. Before printing you will need to fix your STL files using the [[https://service.netfabb.com/login.php Netfabb online service]]. This web-based utility requires a free autodesk account, but after you go through the registration process, you will be able to log in and upload your STL brain file. After a short upload and processing period (a couple of minutes), the website will tell you the file has been processed and provide you with a download link. The file will have the label "_fixed" added to it, so you can easily tell which of your brain files have been checked to ensure printability.

	If you are printing at UB, there is a form you can complete at [[http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html \| this link]].		If you are printing at UB, there is a form you can complete at [[http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html \| this link]].

	If you do not have access to UB's printing facility, there are many web-based companies that will print and mail you 3D prints of files you upload, such as [[http://www.shapeways.com \| Shapeways]] and [[http://www.sculteo.com \| Sculpteo]] (which I have personally used).		If you do not have access to UB's printing facility, there are many web-based companies that will print and mail you 3D prints of files you upload, such as [[http://www.shapeways.com \| Shapeways]] and [[http://www.sculteo.com \| Sculpteo]] (which I have personally used).

Chris: /* 3D Printing */

2019-05-29T16:16:41Z

3D Printing

← Older revision		Revision as of 12:16, 29 May 2019
Line 68:		Line 68:
	If you are printing at UB, there is a form you can complete at [[http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html \| this link]].		If you are printing at UB, there is a form you can complete at [[http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html \| this link]].

	If you do not have access to UB's printing facility, there are ~~no shortage of~~ web-based companies that will print and mail you 3D prints of files you upload, such as [[http://www.shapeways.com \| Shapeways]] and [[http://www.sculteo.com \| Sculpteo]] (which I have personally used).		If you do not have access to UB's printing facility, there are many web-based companies that will print and mail you 3D prints of files you upload, such as [[http://www.shapeways.com \| Shapeways]] and [[http://www.sculteo.com \| Sculpteo]] (which I have personally used).

Chris: /* 3D Printing */

2019-05-29T16:16:26Z

3D Printing

← Older revision		Revision as of 12:16, 29 May 2019
Line 64:		Line 64:

	=3D Printing=		=3D Printing=
	The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files ~~(which Blender will let you directly export any file as that)~~.		The 3D printers at UB use a multitude of files, but all of the printers will accept .stl files. Before printing you will need to fix your STL files using the [[https://service.netfabb.com/login.php \| Netfabb online service]]. This web-based utility requires a free autodesk account, but after you go through the registration process, you will be able to log in and upload your STL brain file. After a short upload and processing period (a couple of minutes), the website will tell you the file has been processed and provide you with a download link. The file will have the label "_fixed" added to it, so you can easily tell which of your brain files have been checked to ensure printability.
	Before printing you will need to fix your STL files using the Netfabb online service (requires a free autodesk account)
	~~https~~://~~service~~.~~netfabb~~.com/~~login~~.~~php~~		If you are printing at UB, there is a form you can complete at [[http://www.buffalo.edu/shared-facilities-equip/Getting-started/DMLworkorder.html \| this link]].

			If you do not have access to UB's printing facility, there are no shortage of web-based companies that will print and mail you 3D prints of files you upload, such as [[http://www.shapeways.com \| Shapeways]] and [[http://www.sculteo.com \| Sculpteo]] (which I have personally used).