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Thursday, January 29, 2015 Search This Blog

How-To: dcm4chee on Ubuntu Search

This article first appeared in Full Circle Magazine, issue #89.

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Maybe this article is not intended for a wide range of people reading this magazine, as I will describe the installation of a
niche software related to the medical and health-care enterprise world. It is not a home software; indeed nobody has a
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positron emission tomography (PET) facility at home, have they?
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and for professional use, it seems something strictly related to information technology, like something made by yum zfs zlogin zones
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anything strictly related to IT, computer science, network and so on
► 2016 (11)
and at last something related to business
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But there are other aspects of Linux and FOSS: the real world, the serious things. Like health care applications, as stated
► Sep (1)
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So, in this article I will explain how to install dcm4chee on Ubuntu. Maybe, as I said before, no reader of this magazine
► Jun (2)
will have the need or the knowledge to install and understand this software, but if you are a student, or if you know a
dentist or a radiological study, maybe you could be inspired by knowing the existence of this software. ► Mar (3)

► Feb (1)
DICOM and PACS ▼ Jan (1)
DICOM (Digital Imaging and Communications in Medicine) “is a standard for handling, storing, printing, and transmitting How-To:
information in medical imaging”. dcm4chee on
Ubuntu
PACS (Picture archiving and communication system) is a medical imaging technology which provides storage of and
access to images from multiple modalities. ► 2014 (17)
 ► 2013 (35)
A modality is a source machine where patient’s images are acquired from, for example, an X-Ray machine or a Magnetic
Resonance scanner. Some other actors of a PACS are: servers, storage (NAS, SAN, tapes), printers, viewers, CD/DVD ► 2012 (26)
robots, etc.

dcm4chee (http://dcm4che.org/) is a DICOM archive and image manager, that is the server side of a PACS system, the
server where medical images (an x-ray, an ultrasound, a magnetic resonance) will be stored, and from which a radiologist
will retrieve your examination in order to carry out a medical report.

“The application contains the DICOM, HL7 services and interfaces that are required to provide storage, retrieval, and
workflow to a health-care environment”. It is written in Java and is prepackaged and deployed within the JBoss
application server. It is open source and licensed under an MPL/GPL/LGPL triple license. There are also a lot of DICOM
related tools provided by the same developers and community (called dcm4che toolkit), and some DICOM viewers, like
Mayam, Oviyam and Weasis.

If you need help and assistance there is a Google group where a vibrant and nice community will be willing to give you
some advice. On the other hand, the wiki lacks a little bit in documentation, that is some pages are dated or are
incomplete.

Let's install it
Even if some willing person has packaged dcm4che in a “.deb” package, and even if I’m a lover of package management
systems, in this case I feel better if I install this software by hand.

So, let’s see how to install dcm4chee on Ubuntu server 14.04 LTS.

First of all we need to install Java. I’m not sure if dcm4chee works with OpenJDK. And I’m not sure if it works with Java
1.7, so let’s install Oracle Java 1.6, using a PPA repository.

sudo apt-get install software-properties-common

sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java6-installer
We need to accept the license, and so on. dcm4chee needs a database: Postgres, DB2, Oracle, MySQL, etc. If you want
to try it without a RDBMS, you can opt for the HSQL package, but let’s install MySQL.

sudo apt-get install mysql-server

Now we need to create a schema and grant all rights to a user.

$ mysql -uroot -p*****

mysql> create schema pacsdb;
mysql> grant all on pacsdb.* to pacs@localhost identified by 'pacs';
mysql> flush privileges;
mysql> \q

Now we need to download JBoss and dcm4chee zip files. Download JBoss 4.2.3.GA (don’t use a newer version!) from
http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA-jdk6.zip/download
Download the latest release of dcm4chee-mysql, 2.18.0 at time of writing, from

http://sourceforge.net/projects/dcm4che/files/dcm4chee/

Put the zip files in a temporary folder, like /var/tmp/dcminstall and unzip them

sudo apt-get install unzip

unzip dcm4chee-2.18.0-mysql.zip
unzip jboss-4.2.3.GA-jdk6.zip

Since we are on a 64-bit operating system, and the dcm4chee zip file contains a 32-bit version of compression library, we
have to download the proper Java Advanced Imaging Image I/O Tools for linux 64-bit from
http://download.java.net/media/jai-imageio/builds/release/1.1/
and replace the Linux version of libclib_jiio.so

wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-
linux-amd64.tar.gz
tar xzvf jai_imageio-1_1-lib-linux-amd64.tar.gz
cp /var/tmp/install/jai_imageio-1_1/lib/libclib_jiio.so /var/tmp/install/dcm4chee-2.18.0-
mysql/bin/native/libclib_jiio.so

Now we have to copy files from JBoss to Dcm4chee:

cd /var/tmp/install/dcm4chee-2.18.0-mysql/bin/
./install_jboss.sh /var/tmp/install/jboss-4.2.3.GA

Now we have to import the provided SQL file in order to create the database tables and indexes:

cd /var/tmp/install/dcm4chee-2.18.0-mysql/sql/
mysql -upacs -ppacs pacsdb < create.mysql

And now we have to move the dcm4chee directory to a definitive place, like /opt, and then it is useful to create a symbolic
link (so, in case of an upgrade, we don’t need to modify any script or anything else pointing to the dcm4chee directory):

cd /
sudo mv /var/tmp/install/dcm4chee-2.18.0-mysql/ /opt/
sudo ln -s /opt/dcm4chee-2.18.0-mysql /opt/dcm4chee

It is a good idea to create a dcm4chee user and change the owner of the installation dir.

useradd dcm4chee
chown -R dcm4chee /opt/dcm4chee-2.18.0-mysql

Now we can try to run dcm4chee in foreground:

su - dcm4chee -c /opt/dcm4chee/bin/run.sh

Using a web browser, connect to http://yourubuntuserver:8080/dcm4chee-web3

The default user is “admin” and the default password is “admin”.

In order to make changes to the default configuration, we need to use the JBoss jmx console
http://yourubuntuserver:8080/jmx-console/, and this task could be painful since there are no manuals covering a step-by-
step configuration: you have to dig inside the wiki and on the old forum or, as I said before, you can call for help in the
mailing list.
More info:
wiki - http://www.dcm4che.org/confluence/display/proj/The+Project

mailing list - https://groups.google.com/forum/m/?hl=en#!forum/dcm4che

discontinued forum - http://forums.dcm4che.org

Tags: article, dcm4chee, dicom, fcm, ubuntu

34 comments:
Anonymous April 13, 2015 at 11:56 AM

Your post is useful. I am playing with DCM4CHE recently as well. I am getting:

No Image Reader for format: rle registered
java.lang.RuntimeException: No Image Reader for format: rle registered
at org.dcm4che3.imageio.codec.ImageReaderFactory.getImageReader(ImageReaderFactory.java:218)
at org.dcm4che3.imageio.plugins.dcm.DicomImageReader.readMetadata(DicomImageReader.java:497)
at org.dcm4che3.imageio.plugins.dcm.DicomImageReader.read(DicomImageReader.java:273)
while reading RLE encoded DICOM file. Do you have any idea about this error? Thanks!

Reply

Replies

Anonymous June 4, 2015 at 11:16 PM

Are you have a OS 32 or 64 bits?

me June 5, 2015 at 9:33 PM

Maybe you are using the 32 bit version of imageio library with 64 bit java, or vice versa

me June 5, 2015 at 9:34 PM

This comment has been removed by the author.

Reply

Anonymous May 29, 2015 at 12:58 PM

Thanks for great article! What you meant by "Now we have to copy files from JBoss to Dcm4chee:" Copy with or
without replace?
Reply

Replies
 me June 5, 2015 at 9:31 PM

I mean that you have to run the install_jboss.sh script.

Maybe I forgot to write this part in this post. I will check asap.

Reply

Anonymous June 29, 2015 at 4:05 PM

Thanks for the article. I was looking for something like this.
Just one question: Where can I dowload the "Java Advanced Imaging Image I/O Tools for linux 64-bit" from? The
link is down and I can't find another option. Thanks.

Reply

Unknown June 30, 2015 at 1:33 PM

Indeed the image-io link is broken. Check this post: https://groups.google.com/forum/m/?

hl=en#!topic/dcm4che/aT5IdPMnh5Q

Reply

rajeshwar rao August 7, 2015 at 5:37 AM

This comment has been removed by the author.

Reply

Unknown September 12, 2015 at 11:09 AM

i had finished all step, but when i runn:

su - dcm4chee -c /opt/dcm4chee/bin/run.sh
i have:
No directory, logging in with HOME=/
run.sh: Missing required file: /opt/dcm4chee/bin/run.jar
please help me!

Reply
 Replies

Unknown November 4, 2015 at 10:33 PM

I have the same problem :S!

Unknown November 4, 2015 at 10:44 PM

I have the same problem :S!

Unknown February 16, 2016 at 11:16 PM

Hi, Maybe you can't create the database structure.

sudo mysql -u root -p pacsdb < create.mysql

Reply

Anonymous October 21, 2015 at 9:21 PM

Your disclaimer "no reader of this magazine will have the need or the knowledge to install and understand this
software" is wrong!

This was great!! Thank you so much for putting these up!

Reply

julioctaboada January 26, 2016 at 12:05 AM

How can I get access to the server from external network if I don't see the standalone.xml file?, I have already
allowed access from anyware to all TCP ports. Thank in advance.

Reply

Anonymous April 25, 2016 at 12:57 PM

Hi,

after this command "su - dcm4chee -c /opt/dcm4chee/bin/run.sh"

system is asking password which one i need to enter

Thanks & regards

Reply

Anonymous April 25, 2016 at 12:58 PM

Hi,

after this command "su - dcm4chee -c /opt/dcm4chee/bin/run.sh" , system is asking password which password i
need to enter?

Thanks & Regards

Reply

Replies

me April 26, 2016 at 11:23 AM

Well, the system user dcm4chee is an application user, like www-data, so it is not necessary to
configure a password for it (via the passwd command or whatever). So i think, if you are not root, that
you must use sudo:
sudo su - dcm4chee -c /opt/dcm4chee/bin/run.sh

Reply

Unknown May 3, 2016 at 9:54 PM

This comment has been removed by the author.

Reply

Anonymous June 13, 2016 at 1:32 PM

just followed your guide and got it working...Some knowledge about Ubuntu in general, MySQL will help. :-)
But got it to work in less then 1 hour.... on vmware in Kubuntu 16.10 with MySql 5.7.12 and in 64bit but kept to
the advised java 1.6.
nice blog. TOP
rgds,
rob

Reply

Replies

Unknown June 13, 2016 at 10:26 PM

You need to change some in your blog.

You are mentioning "Put the zip files in a temporary folder, like /var/tmp/dcminstall and unzip them" but
using "/var/tmp/install" in your command lines

I have tried to run it with the default openJDK 1.8 of Ubuntu 16.10 but the web looks running but the
JBoss jmx console will fail. actually tried with all versions above 1.6 and all failed to show the console
right. the rest gave error messages and showed the code. Probably for the java gurus no challenge
but i am not. So went back to SDK 1.6 and all runs smooth.

Reply

Anonymous June 15, 2016 at 9:40 PM

Can you please give details why not to use with a new version of jboss please

Reply

Replies

Anonymous June 22, 2016 at 1:28 PM

I have read this
"Use neither JBoss 5 nor JBoss 6, because it is completely re-architected and is significantly different
than the 4.2 line of JBoss!" from the dcm4che wiki, sorry for quick question without reading anything
 Reply

Anonymous July 4, 2016 at 11:27 AM

Good tutorial but last step i have an issue

No directory, logging in with HOME=/
run.sh: Missing required file: /opt/dcm4chee/bin/run.jar

could you please help me to run this

Reply

Replies

me July 4, 2016 at 12:58 PM

Which version are you using? The latest one, 2.18.3, lack some files in the bin directory, you have to
copy the missing files from the 2.18.0 release. In addition, do you have issued the install_jboss.sh
script?

Reply

me July 4, 2016 at 12:58 PM

This comment has been removed by the author.

Reply

Unknown September 10, 2016 at 10:16 PM

Hi,
I following exactly per your instructions, installed the same versions as yours, but the image is not showing up in
the dcm4chee when click on Open Image Selection.

Following is the log file.

13:12:43,627 WARN [PatientBean] Coerce null to (0010,0021) Issuer of Patient ID,LO,*1,#22,[Issuer of Patient
ID1 ]
13:12:43,648 INFO [InstanceBean] Created Instance[pk=14,
iuid=1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.848.26, cuid=1.2.840.10008.5.1.4.1.1.7, series-
>ejb/Series:6]
13:12:43,682 INFO [FileBean] Created File[pk=14, 1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.128.22
13:13:03,191 INFO [WADOServlet] 127.0.0.1 - WADO URL:/wado?
requestType=WADO&studyUID=100.118.116.2005.2.1.1143729853.921.5&seriesUID=1.2.826.0.1.3680043.2.15
45.1.2.1.7.20160910.131237.639.21&objectUID=1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.24.23&c
olumns=128
13:13:03,194 INFO [WADOSupport] Get WADO object for
1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.24.23
13:13:03,206 INFO [WADOServlet] 127.0.0.1 - WADO URL:/wado?
requestType=WADO&studyUID=100.118.116.2005.2.1.1143729853.921.5&seriesUID=1.2.826.0.1.3680043.2.15
45.1.2.1.7.20160910.131237.248.24&objectUID=1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.598.25&
columns=128
13:13:03,208 INFO [WADOSupport] Get WADO object for
1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.598.25
13:13:03,219 INFO [WADOServlet] 127.0.0.1 - WADO URL:/wado?
requestType=WADO&studyUID=100.118.116.2005.2.1.1143729853.921.5&seriesUID=1.2.826.0.1.3680043.2.15
45.1.2.1.7.20160910.131237.248.24&objectUID=1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.848.26&
columns=128
13:13:03,220 INFO [WADOSupport] Get WADO object for
1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.848.26
13:13:03,222 INFO [WADOServlet] 127.0.0.1 - WADO URL:/wado?
requestType=WADO&studyUID=100.118.116.2005.2.1.1143729853.921.5&seriesUID=1.2.826.0.1.3680043.2.15
45.1.2.1.7.20160910.131237.248.24&objectUID=1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.109.27&
columns=128
13:13:03,222 INFO [WADOSupport] Get WADO object for
1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.109.27
13:13:03,395 INFO [CacheJournal] M-WRITE /home/wangchuk/Downloads/dcm4chee-2.18.0-
mysql/server/default/wadocachejournal/2016/09/10/13
13:13:03,401 INFO [WADOServlet] send WADO response: image/jpeg
13:13:03,403 INFO [WADOServlet] send WADO response: image/jpeg
13:13:03,402 INFO [WADOServlet] send WADO response: image/jpeg
13:13:03,402 INFO [WADOServlet] send WADO response: image/jpeg
13:13:03,401 INFO [WADOServlet] send WADO response: image/jpeg

Please let me know.

Thank you.
Reply

Unknown September 10, 2016 at 10:21 PM

Hi,
I followed exactly per your instructions, installed the same versions. But image is not showing up in dcm4chee
when click on open image selection. No any error, i noticed in the log file. Following is some part of the log file.

13:13:03,208 INFO [WADOSupport] Get WADO object for

1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.598.25
13:13:03,219 INFO [WADOServlet] 127.0.0.1 - WADO URL:/wado?
requestType=WADO&studyUID=100.118.116.2005.2.1.1143729853.921.5&seriesUID=1.2.826.0.1.3680043.2.15
45.1.2.1.7.20160910.131237.248.24&objectUID=1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.848.26&
columns=128
13:13:03,220 INFO [WADOSupport] Get WADO object for
1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.848.26
13:13:03,222 INFO [WADOServlet] 127.0.0.1 - WADO URL:/wado?
requestType=WADO&studyUID=100.118.116.2005.2.1.1143729853.921.5&seriesUID=1.2.826.0.1.3680043.2.15
45.1.2.1.7.20160910.131237.248.24&objectUID=1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.109.27&
columns=128
13:13:03,222 INFO [WADOSupport] Get WADO object for
1.2.826.0.1.3680043.2.1545.1.2.1.7.20160910.131237.109.27
13:13:03,395 INFO [CacheJournal] M-WRITE /home/wangchuk/Downloads/dcm4chee-2.18.0-
mysql/server/default/wadocachejournal/2016/09/10/13
13:13:03,401 INFO [WADOServlet] send WADO response: image/jpeg
13:13:03,403 INFO [WADOServlet] send WADO response: image/jpeg
13:13:03,402 INFO [WADOServlet] send WADO response: image/jpeg
13:13:03,402 INFO [WADOServlet] send WADO response: image/jpeg
13:13:03,401 INFO [WADOServlet] send WADO response: image/jpeg

Please let me know.

Thanks

Reply

Unknown October 12, 2016 at 8:13 PM

Hello, first of all thanks for the article, and now can you tell me how configure dcm4chee as a service or daemon
Reply

Anonymous October 12, 2016 at 8:14 PM

Hello, first of all thanks for the article, and second, can you tell me how configure dcm4chee as a service or
daemon

Reply

Replies

Ryan Brantley November 2, 2016 at 5:24 PM

From http://www.dcm4che.org/docs/reference/dcm4chee/html/dcm4chee-installation.html

After verifying that the application is installed and running correctly, you may want to install it as a
Windows service or Unix daemon.

Stop the application (type ctrl-c in the console window).

Windows: install dcm4chee as a Windows service executing

DCM4CHEE_DIST/bin/install_service.bat.

Redhat Linux: copy the init script DCM4CHEE_DIST/bin/dcm4chee_init_redhat.sh to /etc/init.d/ and

adjust it according to the dcm4chee installation location, the JDK installation location, and which user
the dcm4chee should run under.

Reply

Unknown October 17, 2016 at 8:35 AM

Nice tutorial,I am using dcmsnd command for sending dicom images with PatientId but image can't going to
specific patient and other patient are able to view data of different patient.
what will be the specific permission and roles for User to perform activities and how to send particular images for
specific patient.
can anyone know..?
Thanks in advance.
 Reply

Unknown November 2, 2016 at 9:58 PM

Hello,

Maybe someone can help me, how create CD/DVD from DCM4CHEE autorun using weasis viewer.

thanks

Reply

Anonymous February 21, 2018 at 4:37 PM

I installed DCM4chee and I use wildfly as a server, how do I connect them?

Reply

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