Editing Scanco User Instructions (section)

==Get Your Files==
===MAC/Linux Options===
====Fetch====
#Download and install [http://fetchsoftworks.com/fetch/|'''Fetch''']
#*This program is free for university staff and students. 
#Fill out [http://fetchsoftworks.com/fetch/free|'''a form''']. 


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====FTP from Terminal====
#Open a terminal
#*MAC: open the "Applications" folder, choose "Utilities", then "Terminal".
#Navigate to where you want to transfer the files to.
#Connect to the micro-CT ftp server using the ftp command in the terminal:
#*Login with the micro-CT user account and password.
#Navigate to the directory of interest on the micro-CT system.
#*Logicals such as "ur" can be used as short cuts. Whole directory names must be used.
#Set a filename mapping convention to remove OpenVMS version numbers.
#*The command <code>ftp> nmap $1;$2 $1</code> sets anything before the version number to parameter $1 and anything after the version number to $2. The file output will be set to $1, therefore the version number will not be kept. 
#Set the file transfer mode.
#*[[File:Important.JPG|20px]] If you transfer an .AIM file in ascii mode, you will receive a "mesh generation" errors and "material ID out of range" message.
#Transfer your files.
#*Option: Turn off prompt so does not ask you whether or not to transfer each file.
#*If you do not turn off the prompt prior to transferring the files, press "a" (for all) to transfer all files at once.
#Exit FTP.

<pre>
$ FTP 136.159.74.231	              !Connect to an FTP Server. Need to input user name and password.	
$ FTP emily.ucalgary.ca	              !Connect to an FTP Server. Need to input user name and password.	
$ FTP microct@emily.ucalgary.ca       !Connect to an FTP Server. Need to input password. 

FTP> cd ur                            !Navigate to the directory containing the target files.
FTP> cd sys$scratch                   !Navigate to the directory containing the target files.

FTP> nmap $1;$2 $1                    !Set a filename mapping convention to remove OpenVMS version numbers.

FTP> bin	                      !Set transfer mode to binary (.aim, .gobj, .isq, and most image file types).
FTP> ascii	                      !Set transfer mode to ascii (.txt, .log, .com, .ps, .pdf and all other files in general).

FTP> put test.aim                     !Put the file
FTP> get test.aim                     !Get the file

FTP> prompt                           !Interactive mode off before transferring multiple files without having to be prompted.
FTP> mput *.aim	                      !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim	                      !Get all files with the .aim extension from the FTP server (mget = multiple get).
FTP> mget *.aim;	              !Transfer the latest version of all aim files in a directory.

FTP> quit	                      !Disconnect from the FTP Server.
</pre>
 

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===Windows Options===
====Scanco Medical µCT FTP====
#Downlod '''Scanco Medical MicroCT FTP 3.4''' from BoydDrive:\\04 - Resources\04 - Software\Scanco Medical MicroCT FTP 3.4\
#Install the software using the default parameters.
#Click on FTP Connection and input the host to connect to, the username, password. 
#Give this profile a name.
#:[[File:Microct_FTP_pic01.jpg|600px]]
#Click on the options tab to set the locations to connect to (e.g., project disk, scratch) and the location on your computer to transfer files to.
#:[[File:Microct_FTP_pic02.jpg|600px]]
#Go back to FTP Connection and press the Connect button.  
#*If you are connecting from off campus to the XtremeCT you will need to use the VPN to gain access through the firewall.
#Use the left tree to navigate folders.  
#*Use the file filter to search for specific file types or file names (bottom left).  
#Select files to download and press the Download Selected Files button (bottom right).
#:[[File:Microct_FTP_pic03.jpg|600px]]
#Press the Exit button to disconnect.


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====Filezilla====
#Download '''Filezilla 2.2.32''' from BoydDrive:\\04 - Resources\04 - Software\Filezilla 2.2.32\  
#*This version of Filezilla will remove the OpenVMS version number from files, the new version will not! 
#*The left side of the program shows your computer, the right side will show the micro-CT system once you have connected.
#:[[File:Filezilla_pic01.jpg|500px]]
#On the top menu, choose "File", then "Site Manager".  
#Create a "New Site" for all the directories that you frequently access.  
#*Give the site a meaningful name.  
#*For the host, you may connect to "emily.ucalgary.ca" or "sceval.ucalgary.ca".   
#*For the logon type choose "Normal" and input the micro-CT user name and password.
#:[[File:Filezilla_pic02.jpg|400px]]
#Click on the "Advanced..." button to set the default remote directory (i.e., on the micro-CT system).
#Set the default local directory if there is a specific location you plan to always transfer files to. 
#Setup any additional sites you want then press "Save and Exit".
#:[[File:Filezilla_pic03.jpg|300px]]
#To connect to a session, hold the left mouse button down over the arrow next to the site manager button (computer icon under "File") to bring up your list of sites.  Highlight the site of interest then release the mouse button to connect.  
#Once connected, you can drag and drop files from the remote site to your local computer.


;*Common FTP locations
{| class="wikitable"
|-
! scope="col"| Account
! scope="col"| Location
! scope="col"| Path
|-
| microct / vivact ||	Data Disk	||DISK2:[MICROCT.DATA]
|-
| microct / vivact ||	Projects Disk	||DISK3:[MICROCT.PROJECTS]
|-
| microct / vivact ||	Scratch Disk	||ADISK1:[MICROCT.SCRATCH]
|-
| invivo / invitro ||	Data Disk	||DISK4:[BONELAB.DATA]
|-
| invivo / invitro ||	Projects Disk	||DISK5:[BONELAB.PROJECTS]
|-
| invivo / invitro ||	Scratch Disk	||ADISK1:[BONELAB.SCRATCH]
|}


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