Difference between revisions of "Dicom"

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(Share File Systems with Mac)
 
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Here are some ways to access the Hoffman2 Cluster login nodes.
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Here are some ways to access the Dicom server.
  
 
==SSH - Command Line==
 
==SSH - Command Line==
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where login_id is replaced by your user account ID.
 
where login_id is replaced by your user account ID.
 
The server host name will be sent by email when you receive your account.
 
The server host name will be sent by email when you receive your account.
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After login, you will be under your home directory, /user/userid/
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To access the group directory, using
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cd /path/to/group_directory
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(/path/to/group_directory should be sent to you together with your account information)
  
 
===Windows===
 
===Windows===
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Using [https://www.hoffman2.idre.ucla.edu/access/login/ Putty] for SSH terminal
 
Using [https://www.hoffman2.idre.ucla.edu/access/login/ Putty] for SSH terminal
  
==Share File Systems with Mac==
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==Sharing File Systems with Mac==
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You can mount Dicom file system to your local Mac computer using SSHFS
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Please follow this similar [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Sharing_Filesystems instruction] for Hoffman2
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Usage:
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sshfs -o idmap=user -o uid=1010 -o gid=20 userid@dicomserver:/path/to/groupdir ~/MOUNTPOINT
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==Copy files to Hoffman2==
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===From SSH command line===
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scp -r dicomuserID@dicomserver:/path/to/group_directory/subject hoffmanID@hoffman2.idre.ucla.edu:/path/to/your_directory/
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or
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rsync -av dicomuserID@dicomserver:/path/to/group_directory/subject hoffmanID@hoffman2.idre.ucla.edu:/path/to/your_directory/
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===Script ===
  
You can mount Dicom file system to your local Mac computer.
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[https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Scripts:setup_subject setup_subject] script is used to copy files from Dicom to Hoffman2, and do other processing such as nifti convert.
Please follow this similar [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Sharing_Filesystems instruction]
 

Latest revision as of 18:16, 10 June 2019

To apply for a Dicom server account,

Send email with the following information to the CCN system admin:

1. Your Hoffman2 account ID if you have one.

2. CC your request to the PI whose group directory you need access to for approval.


Here are some ways to access the Dicom server.

SSH - Command Line

Mac/Linux/Unix

Simple SSH

Use the ssh command from a terminal:

ssh login_id@dicomservername

where login_id is replaced by your user account ID. The server host name will be sent by email when you receive your account.

After login, you will be under your home directory, /user/userid/

To access the group directory, using

cd /path/to/group_directory

(/path/to/group_directory should be sent to you together with your account information)

Windows

Using Putty for SSH terminal

Sharing File Systems with Mac

You can mount Dicom file system to your local Mac computer using SSHFS

Please follow this similar instruction for Hoffman2

Usage:

sshfs -o idmap=user -o uid=1010 -o gid=20 userid@dicomserver:/path/to/groupdir ~/MOUNTPOINT

Copy files to Hoffman2

From SSH command line

scp -r dicomuserID@dicomserver:/path/to/group_directory/subject hoffmanID@hoffman2.idre.ucla.edu:/path/to/your_directory/

or

rsync -av dicomuserID@dicomserver:/path/to/group_directory/subject hoffmanID@hoffman2.idre.ucla.edu:/path/to/your_directory/

Script

setup_subject script is used to copy files from Dicom to Hoffman2, and do other processing such as nifti convert.