Dicom: Difference between revisions
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To apply for a Dicom server account, | To apply for a Dicom server account, | ||
Send email with the following information to the CCN | Send an email with the following information to the CCN Programmer Analyst [mailto:jonhernandez@mednet.ucla.edu Jonathan Hernandez]. | ||
1. Your Hoffman2 account ID if you have one. | 1. Your Hoffman2 account ID if you have one. | ||
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ssh login_id@dicomservername | ssh login_id@dicomservername | ||
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. For CCN, it should be dcm.semel.ucla.edu. You will then need to enter your dicom server password. | ||
After login, you will be under your home directory, /user/userid/ | After login, you will be under your home directory, /user/userid/ | ||
To access the group directory, | To access the group directory, use | ||
cd /path/to/group_directory | cd /path/to/group_directory | ||
(/path/to/group_directory should be sent to you together with your account information) | (/path/to/group_directory should be sent to you together with your account information) | ||
For CCN, this will be /data/dicom/your_lab_folder_name | |||
===Windows=== | ===Windows=== | ||
Use [https://www.hoffman2.idre.ucla.edu/access/login/ Putty] for SSH terminal. See [https://www.hoffman2.idre.ucla.edu/Using-H2/Connecting/Connecting.html Hoffman's documentation] for instructions on how to connect and set up functionality (such as running GUI applications). | |||
==Sharing File Systems with Mac== | ==Sharing File Systems with Mac== | ||
You can mount Dicom file system to your local Mac computer using SSHFS | You can mount the Dicom file system to your local Mac computer using SSHFS | ||
Please follow | Please follow these similar [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Sharing_Filesystems instructions] for Hoffman2 | ||
Usage: | Usage: | ||
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==Copy files to Hoffman2== | ==Copy files to Hoffman2== | ||
Please note that copying files off the Dicom server takes much longer when the scanner is in active use, due to the system prioritizing incoming data. As such, you may want to check the scanner calendar and wait for off hours or gaps in the schedule to do your download. | |||
===From SSH command line=== | ===From SSH command line=== | ||
scp -r dicomuserID@dicomserver:/path/to/group_directory/subject | After login to Hoffman2, run one of the following commands from one of the Hoffman2 server | ||
scp -r dicomuserID@dicomserver:/path/to/group_directory/subject /path/to/your_directory/ | |||
or | or | ||
rsync -av dicomuserID@dicomserver:/path/to/group_directory/subject | rsync -av dicomuserID@dicomserver:/path/to/group_directory/subject /path/to/your_directory/ | ||
===Script === | ===Script === | ||
[https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Scripts:setup_subject_3 setup_subject] script is used to copy files from Dicom to Hoffman2, and do other processing such as nifti convert. | [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Scripts:setup_subject_3 setup_subject] script is used to copy files from Dicom to Hoffman2, and do other processing such as nifti convert. | ||
Revision as of 18:56, 1 March 2024
To apply for a Dicom server account,
Send an email with the following information to the CCN Programmer Analyst Jonathan Hernandez.
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. For CCN, it should be dcm.semel.ucla.edu. You will then need to enter your dicom server password.
After login, you will be under your home directory, /user/userid/
To access the group directory, use
cd /path/to/group_directory
(/path/to/group_directory should be sent to you together with your account information) For CCN, this will be /data/dicom/your_lab_folder_name
Windows
Use Putty for SSH terminal. See Hoffman's documentation for instructions on how to connect and set up functionality (such as running GUI applications).
Sharing File Systems with Mac
You can mount the Dicom file system to your local Mac computer using SSHFS
Please follow these similar instructions for Hoffman2
Usage:
sshfs -o idmap=user -o uid=1010 -o gid=20 userid@dicomserver:/path/to/groupdir ~/MOUNTPOINT
Copy files to Hoffman2
Please note that copying files off the Dicom server takes much longer when the scanner is in active use, due to the system prioritizing incoming data. As such, you may want to check the scanner calendar and wait for off hours or gaps in the schedule to do your download.
From SSH command line
After login to Hoffman2, run one of the following commands from one of the Hoffman2 server
scp -r dicomuserID@dicomserver:/path/to/group_directory/subject /path/to/your_directory/
or
rsync -av dicomuserID@dicomserver:/path/to/group_directory/subject /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.