CCN Wiki - User contributions [en]

3D Brain Models

2019-03-06T05:33:00Z

Ccnlab: /* First */

This page is all about turning FreeSurfer surface files into 3D printable models.
Inspiration comes from [https://brainder.org/2012/05/08/importing-freesurfer-cortical-meshes-into-blender/ here]

=Free Surfer=

==Blender==
After creating the pial layer hemisphere's in FreeSurfer, you're next going to want to import one file at a time into Blender. Once the file has been imported there should be a gray brain mesh on the screen in Blender. To make working with the mesh easier you can change it's size by going to the bottom left-hand side of the page and change the X, Y, and Z coordinates to 1.0. Once they are all at 1.0 the brain will be much smaller and fit nicely within the provided grid. You can use the rotate and transform tools on the left-hand side of the screen to move and change the direction of the brain. To the best of your ability, try to get the brain level on all planes in a way similar to it's real life orientation. After the first hemisphere is in place do the exact same process with the other hemisphere. Once both halves are of the same size and orientation, try to align them next to each other as best as possible and join the halves into one object by right clicking on one half, then hold shift down and right click on the other. After both hemispheres are selected you just have to press CTRL + J, and the two halves should become one mesh.
===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).

3D Brain Models

2019-03-06T05:17:10Z

Ccnlab: /* First */

2018-02-28T22:37:45Z

2018-02-28T22:23:41Z

Ccnlab: /* Plasticity */

Developmental Neuroscience

2018-02-28T22:23:19Z

Ccnlab: /* temp */

==Overview==

===Principles===

===Individual Differences===

===Disorders===

==Synapses==

===Epigenetics===

===Circuit Development===

==Plasticity==

===Homeostatic Plasticity===

===Functional Plasticity===

===Sensory Plasticity===

===Sensitive Periods===

===Environmental Enrichment===

====temp====

=====temp=====

======temp======

==Formatting Guide==
Click [https://www.mediawiki.org/wiki/Help:Formatting here] for a guide to formatting using wiki markup.

2016-04-21T20:44:18Z

Ccnlab: /* File transfer over SSH */

SSH

2016-04-21T20:41:42Z

Ccnlab: /* SCP */

'''SSH''' stands for '''S'''ecure '''SH'''ell. More information about SSH can be found [https://en.wikipedia.org/wiki/Secure_Shell here], but in a nutshell, it is an encrypted connection to a Unix/Linux terminal. Because much of what we do in the lab is done through the terminal, connecting to our lab computers via SSH allows you to get things done without being physically in the lab.

In order to connect via SSH, you will need an SSH client, and different operating systems will use different SSH clients. Though there are many alternatives, suggested clients are provided below.

== Windows ==
The suggested SSH client for computers running Windows is called [http://putty.org/ PuTTY ], and the latest version of the program can be found [http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe here]. This program does not need to install a bunch of files or modify your computer in any way in order to run. Simply download putty.exe, copy (or move) this file to whichever directory you prefer (e.g., C:\Windows\Program Files x86\PUTTY\) and launch it.

Note that the fact that this simple program doesn't do a big installation song and dance is a blessing and a curse: It's really compact and doesn't muck up your computer with stuff you don't want. On the other hand, you won't have the benefit of having a handy Start Menu shortcut being created for you. You will either have to find the putty.exe file on your computer each time you want to connect, or else create a menu or desktop shortcut manually.

=== Connecting in PuTTY ===
When you launch PuTTY, you will see a configuration window similar to the one below:

[[File:Putty_settings.png]]

The important information you need to know are the Host Names (or IP addresses) of the computers you wish to connect to. In our lab, we have two workstations, ''wernickesarea'' and ''brocasarea''.

#To connect to either of them, you need to enter the IP address for either wernickesarea (<code>128.205.173.202</code>) or for brocasarea (<code>128.205.172.41</code>) into the first box (in the image above, replace ''example.com'' with the appropriate IP address)
#When you have done so, click the '''Open''' button.
#If this is your first time connecting to a particular computer, you will see a window labeled '''PuTTY Security Alert'''. Just hit the '''Yes''' button. All this window is saying is that the program does not yet have the encryption key being used by the computer you are talking to (this warning is to alert you to the potential for certain types of hacks).
#Once the SSH Connection is open, you should see a terminal prompt asking for your username (this will likely be your first name)
#*Enter your username and hit the '''Enter''' key
#Next, you will be asked to enter your password
#*Enter your password and hit the '''Enter''' key
#*Please note that you will NOT see your cursor moving, or any characters typed (such as ******), when typing your password. This is a standard PuTTY security feature.

Assuming your username/password credentials check out, you will now find yourself with a terminal connection and in your home directory, just as though you are logged in and have launched a new terminal window. You can use this terminal window to perform any tasks that do not launch applications that have a graphical user interface. For example, you can use a text editor like <code>nano</code> to edit and run a script, or check on the progress of some ongoing process.

==Mac OSX==
The good news is that OSX is Unix/Linux under the hood, and that you already have a command-line SSH client installed. In fact, it's slightly more flexible because you can use it to launch programs that have a graphical interface (although you might find some programs run too slowly over the internet to be very useful).

===Connecting with the ssh command===
#Open up a terminal window
#*If you have never done this, you will find it under '''Applications/Utilities/Terminal'''
#In your terminal window, type <code>ssh 128.205.xxx.yyy</code>, where xxx.yyy depend on whether you wish to connect to brocasarea or wernickesarea (see the IP addresses above in the instructions for Windows users)
#You will be prompted for your username and your password

After a successful login, you will find yourself with a terminal connection and in your home directory, just as though you had logged in and launched a terminal window on one of the computers in the lab.

===Connecting with the ssh command using Xwindows===
The Xorg window server is the system that Unix computers use to draw windows and other graphic elements on the screen. If you have an Xorg client installed on your Mac OSX computer, you can have your local screen accept these graphical instructions from the remote computer. This would let you run remote applications that have a graphical user interface. To use X, simply use the -X command line switch when connecting (that's an upper-case X):
<code>ssh -X 128.205.xxx.yyy</code>
====Where can I get an Xorg client?====
The OSX Xorg client is calle XQuartz (homepage: [http://www.xquartz.org/ www.xquartz.org]). If you go to that website, you can download the .dmg installer.
====Is a connection that uses Xorg slow?====
Yep.

But I've done it many times now from my kitchen table to use simple text editors, and it hasn't been too ridiculous. On the other hand, it probably isn't a practical way to edit 3D fMRI data (but it can handle MATLAB scripts running SPM pretty well).

=== File transfer over SSH ===
You can use SSH as a handy means of transferring files. SFTP is a Secure File Transfer Protocol over SSH.

==Linux==
See the instructions for OSX. Also, don't be daft. If you've committed to Linux, you probably already know how to do this.

==SCP==
'''SCP''' stands for '''S'''ecure '''C'''o'''p'''y, which is a quick and easy way to transfer files to and from multiple machines. Below are examples for transferring files in a variety of situations. Use an IP address for Broca's, Wernicke's, etc. in place of "remotehost" below. If you are using windows SSH, or are already using an SSH connection, the localhost is the host on which you are currently connected. On linux (and probably Mac OSX) the scp command functions independently from ssh (like SFTP).

Copying a file from a remote host to a local host:
<code>scp your_username@remotehost:directory/filename /some/local/directory </code>

Copying a file from a local host to a remote host:
<code>scp directory/filename your_username@remotehost:/some/remote/directory </code>

Copying a file(s) from a local host to your home folder on a remote host:
<code>scp filename1 filename2 your_username@remotehost:~ </code>

Copying a file from one remote host to another remote host:
<code>scp your_username@remotehost1:/some/remote/directory/filename \
your_username@remotehost2:/some/remote/directory/ </code>

Copying multiple files from a remote host to your current local directory
<code>scp your_username@remotehost:/some/remote/directory/\{filename1,filename2,filename3\}</code>

Copying multiple files from your home folder on a remote host to your current local directory
<code>scp your_username@remotehost:~/\{filename1,filename2\}</code>

If you want to transfer a folder, you'll first need to compress it recursively.

With Zip:
<code>zip -r foldername.zip foldername</code>

Or with Tar:
<code>tar -zcvf foldername.tar.gz foldername</code>

SSH

2016-04-21T20:37:51Z

Ccnlab: /* SCP */

'''SSH''' stands for '''S'''ecure '''SH'''ell. More information about SSH can be found [https://en.wikipedia.org/wiki/Secure_Shell here], but in a nutshell, it is an encrypted connection to a Unix/Linux terminal. Because much of what we do in the lab is done through the terminal, connecting to our lab computers via SSH allows you to get things done without being physically in the lab.

In order to connect via SSH, you will need an SSH client, and different operating systems will use different SSH clients. Though there are many alternatives, suggested clients are provided below.

== Windows ==
The suggested SSH client for computers running Windows is called [http://putty.org/ PuTTY ], and the latest version of the program can be found [http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe here]. This program does not need to install a bunch of files or modify your computer in any way in order to run. Simply download putty.exe, copy (or move) this file to whichever directory you prefer (e.g., C:\Windows\Program Files x86\PUTTY\) and launch it.

Note that the fact that this simple program doesn't do a big installation song and dance is a blessing and a curse: It's really compact and doesn't muck up your computer with stuff you don't want. On the other hand, you won't have the benefit of having a handy Start Menu shortcut being created for you. You will either have to find the putty.exe file on your computer each time you want to connect, or else create a menu or desktop shortcut manually.

=== Connecting in PuTTY ===
When you launch PuTTY, you will see a configuration window similar to the one below:

[[File:Putty_settings.png]]

The important information you need to know are the Host Names (or IP addresses) of the computers you wish to connect to. In our lab, we have two workstations, ''wernickesarea'' and ''brocasarea''.

#To connect to either of them, you need to enter the IP address for either wernickesarea (<code>128.205.173.202</code>) or for brocasarea (<code>128.205.172.41</code>) into the first box (in the image above, replace ''example.com'' with the appropriate IP address)
#When you have done so, click the '''Open''' button.
#If this is your first time connecting to a particular computer, you will see a window labeled '''PuTTY Security Alert'''. Just hit the '''Yes''' button. All this window is saying is that the program does not yet have the encryption key being used by the computer you are talking to (this warning is to alert you to the potential for certain types of hacks).
#Once the SSH Connection is open, you should see a terminal prompt asking for your username (this will likely be your first name)
#*Enter your username and hit the '''Enter''' key
#Next, you will be asked to enter your password
#*Enter your password and hit the '''Enter''' key
#*Please note that you will NOT see your cursor moving, or any characters typed (such as ******), when typing your password. This is a standard PuTTY security feature.

Assuming your username/password credentials check out, you will now find yourself with a terminal connection and in your home directory, just as though you are logged in and have launched a new terminal window. You can use this terminal window to perform any tasks that do not launch applications that have a graphical user interface. For example, you can use a text editor like <code>nano</code> to edit and run a script, or check on the progress of some ongoing process.

==Mac OSX==
The good news is that OSX is Unix/Linux under the hood, and that you already have a command-line SSH client installed. In fact, it's slightly more flexible because you can use it to launch programs that have a graphical interface (although you might find some programs run too slowly over the internet to be very useful).

===Connecting with the ssh command===
#Open up a terminal window
#*If you have never done this, you will find it under '''Applications/Utilities/Terminal'''
#In your terminal window, type <code>ssh 128.205.xxx.yyy</code>, where xxx.yyy depend on whether you wish to connect to brocasarea or wernickesarea (see the IP addresses above in the instructions for Windows users)
#You will be prompted for your username and your password

After a successful login, you will find yourself with a terminal connection and in your home directory, just as though you had logged in and launched a terminal window on one of the computers in the lab.

===Connecting with the ssh command using Xwindows===
The Xorg window server is the system that Unix computers use to draw windows and other graphic elements on the screen. If you have an Xorg client installed on your Mac OSX computer, you can have your local screen accept these graphical instructions from the remote computer. This would let you run remote applications that have a graphical user interface. To use X, simply use the -X command line switch when connecting (that's an upper-case X):
<code>ssh -X 128.205.xxx.yyy</code>
====Where can I get an Xorg client?====
The OSX Xorg client is calle XQuartz (homepage: [http://www.xquartz.org/ www.xquartz.org]). If you go to that website, you can download the .dmg installer.
====Is a connection that uses Xorg slow?====
Yep.

But I've done it many times now from my kitchen table to use simple text editors, and it hasn't been too ridiculous. On the other hand, it probably isn't a practical way to edit 3D fMRI data (but it can handle MATLAB scripts running SPM pretty well).

=== File transfer over SSH ===
You can use SSH as a handy means of transferring files. SFTP is a Secure File Transfer Protocol over SSH.

==Linux==
See the instructions for OSX. Also, don't be daft. If you've committed to Linux, you probably already know how to do this.

==SCP==
'''SCP''' stands for '''S'''ecure '''C'''o'''p'''y, which is a quick and easy way to transfer files to and from multiple machines. Below are examples for transferring files in a variety of situations. Use an IP address for Broca's, Wernicke's, etc. in place of "remotehost" below. If you are using windows SSH, or are already using an SSH connection, the localhost is the host on which you are currently connected. On linux (and probably Mac OSX) the scp command functions independently from ssh (like SFTP).

Copying a file from a remote host to a local host:
<code>scp your_username@remotehost:directory/filename /some/local/directory </code>

Copying a file from a local host to a remote host:
<code>scp directory/filename your_username@remotehost:/some/remote/directory </code>

Copying a file(s) from a local host to your home folder on a remote host:
<code>scp filename1 filename2 your_username@remotehost:~ </code>

Copying a file from one remote host to another remote host:
<code>scp your_username@remotehost1:/some/remote/directory/filename \
your_username@remotehost2:/some/remote/directory/ </code>

Copying multiple files from a remote host to your current local directory
<code>scp your_username@remotehost:/some/remote/directory/\{filename1,filename2,filename3\}</code>

Copying multiple files from your home folder on a remote host to your current local directory
<code>scp your_username@remotehost:~/\{filename1,filename2\}</code>

If you want to transfer a folder, you'll first need to compress it recursively.

With Zip
zip -r filename.zip filename

Or with Tar
tar -z

File:Example.docx

2016-02-23T21:29:28Z

Ccnlab:

File:Example.docx

2016-02-23T21:25:00Z

Ccnlab: Ccnlab uploaded a new version of File:Example.docx

File:Example.docx

2016-02-23T21:24:37Z

Ccnlab: Ccnlab uploaded a new version of File:Example.docx

2016-02-23T20:53:51Z

Ccnlab:

Main Page

2016-02-23T20:53:41Z

Ccnlab:

Welcome to the CCN Lab Wiki.

[[File:cpicard.jpg]]

== Terminal Commands & Other Lab Stuff ==
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=ubmount UBFS and ubmount]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=SSH Using SSH]

== Data Analysis ==
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=FreeSurfer FreeSurfer Pipeline]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=SPM SPM Pipeline]

== Experiment A to Z ==
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=Participant_Triage Participant Triage]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=Pre-fMRI_Scanning_Protocol Pre-fMRI Scanning Protocol]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=Participant_Instructions Participant Instructions]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=MRI_Prep MRI Prep (Prior to scan date)]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=MRI_Setup MRI Setup]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=MIKENET MIKENET Neural Network C Library Setup]

== MediaWiki - Guides for Getting started ==

* [//www.mediawiki.org/wiki/Help:Formatting Useful Formatting Guide]
* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Main Page

2016-02-23T20:46:06Z

Ccnlab:

Welcome to the CCN Lab Wiki.

[[File:cpicard.png]]

== Terminal Commands & Other Lab Stuff ==
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=ubmount UBFS and ubmount]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=SSH Using SSH]

== Data Analysis ==
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=FreeSurfer FreeSurfer Pipeline]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=SPM SPM Pipeline]

== Experiment A to Z ==
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=Participant_Triage Participant Triage]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=Pre-fMRI_Scanning_Protocol Pre-fMRI Scanning Protocol]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=Participant_Instructions Participant Instructions]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=MRI_Prep MRI Prep (Prior to scan date)]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=MRI_Setup MRI Setup]
* [//ccnlab.psy.buffalo.edu/wiki/index.php?title=MIKENET MIKENET Neural Network C Library Setup]

== MediaWiki - Guides for Getting started ==

* [//www.mediawiki.org/wiki/Help:Formatting Useful Formatting Guide]
* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Main Page

2016-02-23T19:57:42Z

Ccnlab: