Pablo Sau
May 2005
This document try to offer information of how get the best use of the cdmedic-6.2.iso software, serving as introduction to Free Medical Imaging Software in Linux environment.
This software is appropriate for Radiologists, Nuclear medicine and Radiotherapy Physicians and MD, Neurologists and Neurosurgeons and also other branches related to Medical imaging as Physics and Informatica.
This document uses the following conventions:
| Descriptions | Appearance |
|---|---|
| Warnings |  Warning |
| Hint |  Hint |
| Notes |  Note |
| Information requiring special attention |  Warning |
| File Names | file.extension |
| Directory Names | directory |
| Commands to be typed | command |
| Applications Names | application |
| Prompt of users command under bash shell | bash$ |
| Prompt of root users command under bash shell | bash# |
| Menus | MENU->SUBMENU->SUBSUBMENU |
| Environment Variables | VARIABLE |
| Emphasized word | word |
| Pressed keys | ENTER, CTRL, ALT,SHIFT,F2.. |
Comments on this Guide may be directed to the author PabloSau@cdmedic.com, all suggestions are welcome and possible collaborations even better.
Thanks to everyone that contributed to the development of free software, and shared effort and experience with all world.
In less than five minutes you can have the CDMEDIC up and running, of course without having in account the downloading time.
No really necessary to be a LINUX or DICOM guru, this guide is intended to cope with normal PC users and serve as introduction to the Linux, DICOM and the free Medical software.
PC Intel-compatible CPU (i486 or later) at least 96 MB of RAM (128 MB or more RAM is recommended) with bootable CD-ROM drive, or a boot floppy and standard CD-ROM (IDE/ATAPI or SCSI), standard SVGA-compatible graphics card and serial or PS/2 standard mouse or IMPS/2-compatible USB-mouse.
Download cdmedic-6.2.iso from http://cdmedicpacsweb.sourceforge.net (md5sums: b4981f20f312964df2ed09f0212f9038) image and burn a CD ROM with your favorite program.
Ask your net administrator for a free local net IP direction , net mask and gateway if available, and IP directions , AEs and ports of each modality to be connected to the CDMEDICPACSWEB.
To boot from CD ROM you must configure the BIOS usually by pressing the DEL key when the PC is starting or the F2 key in laptops, if either doesn't work, please refer to yours PC manual. If its impossible in your PC to boot from the CDROM you must create a boot floppy with the image boot.img from the directory KNOPPIX of the CDROM, in Linux with the command dd if=/CDROM/KNOPPIX of=/dev/fd0 and in windows with the program rawrite included in that directory
Once restarted the PC with the CDMEDIC CDROM, you'll get the boot: prompt , just press the ENTER key , and wait a couple of minutes to have the KDE3 window manager running, during this time you can see the messages relate to the hardware detection progress .
If after booting messages you only get
a black screen, the problem probably is related to the supported
Vertical
Refresh Frequency(VRF) of the Monitor, so reboot by pressing the RESET
button of the PC or press CNTRL+ ALT+ SUPR
keys, after that
type at the boot: knoppix xvrefresh=60 ENTER
.If the Monitor supports more than 60Hz of VRF then try boot:
knoppix xserver=fbdev ENTER
If you have got a wheel mouse, then you
can activate it by typing at the boot: knoppix wheelmouse
ENTER, more options pressing F2 at the boot:
prompt.
Once you have the KDE3 window manager running you'll want to configure the net to have access to Internet and to the modalities to import DICOM images from them. If your net has a DHCP server you'll get the network settings automaticly and have Internet and LAN connection available. If your net hasn't DHCP server running you must configure the net parameters clicking the CONF icon or Menu K -> KNOPPIX->Network/Internet->Network card configuration and input your local net parameters .
Normally local net has IP like 192.168.1.20
, NETMASK like 255.255.255.0, BROADCAST ADDRESS like 192.168.1.255
and GATEWAY like 192.168.1.1, and NAMESERVER 195.235.113.3
195.235.96.90
Try to navigate Internet clicking the Mozilla icon or Open a terminal clicking the monitor icon at the bottom bar or Menu K->KNOPPIX->Root Shell , and type at the bash# prompt ping WWW.google.com or other Internet or local net IP address.
If you have the net auto-configured
and you can ping the local net but you have not access to Internet,
probably the problem relates to the gateway configuration, so
reconfigure
the net manually with the correct settings.
Now you can save your configuration to avoid to reconfigure every time you restart the PC. Menu K->Configure-> Save KNOPPIX configuration, you can choose what configuration to save and where, floppy or hard disk partition, in the later case a file is created in that partition without alter other contents of that partition.
To recover in the next boot the
configuration
you must type at the boot: knoppix myconfig=scan
Click on the CONF icon or Menu K->DICOM->PACS Conf , enter the local AE Title, is the DICOM name of your PC, enter the remote AE Title and its IP and port (104 frequently used), and also the remote modality must be configured with the PC AE and PC IP (the PC port is 10004) to achieve DICOM connectivity.
Once you have configured the DICOM
connectivity
you loose the access to the DICOM samples that you can see clicking
the PACS icon, typing ANONYMOUS in the Patient name field and after
that clicking the Search button.
Click once more in the PACS icon or Menu K->DICOM->PACS Conf , the Mozilla Web browser will open with the Configured DICOM Nodes page, click the status link and you must get 0% packet loss from ping remote modality and Successful operation from DICOM_echo, the you are ready to receive DICOM studies from the remote modality.
Supposed you have stored DICOM images, processed them or created documents, you now can save your work in an hidden file in your windows partition or other partition, even in an encrypted manner or if you have a dedicated partition, you can use the whole of it.
Menu K->KNOPPIX->Make KNOPPIX Persistent Home and follow the instructions.
To recover in the next boot your work you
must type at the boot: knoppix home=scan
Now you have the possibility of install the software in the hard disk, Menu K->KNOPPIX->KNOPPIX Hard Disk Installation and read carefully the initial caption and it is convenient to have previous experience on LINUX installation.
Not pretending to be exhaustive but introducing the software installed in the cdmedic-6.2.iso and giving some clues to be started with, many programs have a desktop icon to access to their information, and all have their documentation at /usr/share/doc/program_name.
Digital Imaging and Communication in Medicine is the standard in medical imaging format also managing the communications and interoperability between modalities.
The Mallinckrodt Institute of Radiology Central Test Node, ``premiere'' in DICOM software, is a implementation which was designed to be used at the RSNA annual meetings to foster cooperative demonstrations by the medical imaging vendors. The goal was to provide a centralized implementation that facilitated vendor participation based on the evolving DICOM standard.
The CTN home-page at http://wuerlim.wustl.edu/DICOM/ctn.html
You can configure and fine tune the CTN
using the Menu K->DICOM->CTN->CTN Conf
If you want to delete studies from the
PACS you can use the Menu K->DICOM->CTN-> IDB Viewer
You can auto-send studies from the PACS
to a directory and even rename the subdirectories and files opening
a terminal and executing
bash# simple_storage -v -n naming 4006 ENTER
The naming file is a plain text file with
the following format , you can get the group and element tag executing
bash# dcm_print_dictionary and you can use as may D and F labels
as you want.
| /AE Title/Directory/File | Group Tag | Element Tag | #Comment (Don't include this line!) |
|---|---|---|---|
| A | #AE Title | ||
| D | 0010 | 0010 | #Patient Name |
| F | 0008 | 0018 | #SOP Instance UID |
The OFFIS DICOM Toolkit, European Central Test Node of the Oldenburg's University, is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling off-line media, sending and receiving images over a network connection, as well as demonstrative image storage and work-list servers.
The OFFIS DCMTK home-page at http://dicom.offis.de/dcmtk.php.en
Author's software, full featured free PACS based on ctn , dcmtk and
mysql, with remote administration using apache mod perl and imaging
processing capabilities using ImageMagick , Grevera's dcm2pgm DICOM
converter and AFNI, available in Debian packaging format for i386. Now
also added autoconversion from DICOM serie recived at port 4006 to
Analyze format used by AMIDE and FSL and to AFNI format.
The CDMEDIC PACS WEB home-page at http://cdmedicpacsweb.sourceforge.net
Image manipulation program , for photo retouching, image composition and image authoring.
The Gimp home-page at http://www.gimp.org
ImageMagick, robust collection of tools and libraries offered under a usage license to read, write, and manipulate an image in many image formats (over 88 major formats) including popular formats like TIFF, JPEG, PNG, PDF, Photo-CD, and GIF. With ImageMagick you can create images dynamically, making it suitable for Web applications. You can also resize, rotate, sharpen, color reduce, or add special effects to an image or image sequence and save your completed work in the same or differing image format. Image processing operations are available from the command line, as well as through C, C++, Perl, or Java programming interfaces.
The ImageMagick home-page at http://www.imagemagick.org/
To convert between deferents image formats
is so easy as: bash$ convert file.gif file.bmp
And to create an animated gif from several jpgs: bash$ convert file_1.jpg file_2.jpg ... file_n.jpg video.gif , see all options with bash$ man convert
XMedcon is a tool to convert between different Medical Imaging Formats as DICOM, AcrNema, Analyze, InterFile, Ecat, PNG, GIF89, Concorde, INW, Binary and ASCII raw data.
The XMedcon home-page at http://xmedcon.sourceforge.net/
You can create DICOM files, as an example
you can convert from Analyze to DICOM ;
XMedcon Menu File->Open->amide->brain.hdr
Xmedcon Menu File->Save as->DICOM mr000-brain.dcm (you can use the converted file to play with SLICER)
AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
The AFNI home-page at http://afni.nimh.nih.gov/afni/
Clicking the AFNI icon , you launch the
AFNI program with to samples MRI and PET, you select one of them from
Switch Anatomy button,
you can see the Talairach View , and if you want to get the Atlas colors you must press the See TT Sub menu Altlas Regions in the Define Function Sub menu,
then clicking the image with the right button you can use -Talairach to to go to any brain structure or Brodman area or use -Atlas colors to color it.
To volume render the data set AFNI Menu
Define Datamode->Plugins->Render [new]/dataset->Choose
Underlay
Dataset and play with the settings also click the Help button and
The AFNI Doc icon for complete information of AFNI programs.
To convert DICOM to AFNI format if you
have for example 128 slices of a 3D brain in a directory /x/y , execute
bash$cd /x/y && to3d *
FSL is a comprehensive library of functional and structural brain image analysis tools.Most of the tools can be run both from the Unix command line and as GUIs ("point-and-click" graphical user interfaces)
The FSL home-page at http://www.fmrib.ox.ac.uk/fsl/
To work with FSL you need the studies in
the Analyze format , you can create with XMedcon from DICOM for example
or convert from AFNI format using bash$ 3dAFNItoANALYZE analyze.hdr
afni_name
You can segment the brain in a 3D MRI study
FSL->Brain Extraction (You can also use the AFNI 3dIntracranial
command)
and after you can filter it gaining SNR without smooth introduction
with FSL->SUSAN Noise Reduction (Slow process!), and segment CSF,
white an grey matter with FSL->FAST segmentation even measure the
brain atrophy using SIENA, see FSL->HELP for more information.
Amide is a completely free tool for viewing, analyzing, and registering volumetric medical imaging data sets.
The Amide home-page at http://amide.sourceforge.net/
You can see the MRI and PET samples (The
are registered to Talairach Atlas) opening the Amide Menu
File->Import
File (guess)->amide->brain.hdr, repeat with mr.hdr and pet.hdr.
3D Slicer, tool for visualization, registration , segmentation and quantification of medical data.
The Slicer home-page at http://www.slicer.org/
To start playing with Slicer, Menu Add
Volume->Properties->Dicom->Select DICOM Volume-> Change to:
/home/knoppix->
mr000-brain.dcm->OK,
for more information, see Slicer Documentation clicking the Doc 3D Slicer icon.
The Mozilla Firefox Browser is small, fast and easy to use, and offers many advantages over other web browsers, such as the tabbed browsing and the ability to block pop-up windows.
The Mozilla Firefox home page at http://www.mozilla.org/projects/firefox/
The Evolution is a robust and easy to use mail client, similar to competing products like Outlook Express, not only to manage your mail but also to manage your appointments, contacts, but with some major advantages such as junk mail classification.
Evolution User Guide at http://www.novell.com/documentation/ximian.html
Apache has been the most popular web server on the Internet since April of 1996. The May 2003 Netcraft Web Server Survey found that 62% of the web sites on the Internet are using Apache, thus making it more widely used than all other web servers combined.
The Apache home-page at http://www.apache.org/"
If you copy your html web pages to the
directory /var/www them will be available to you local net pointing
the browser to http://your_IP/your_document.html
OpenSSH is a FREE version of the SSH protocol suite of network connectivity tools that encrypts all traffic (including passwords) to effectively eliminate eavesdropping, connection hijacking, and other network-level attacks.
Open ssh home-page at http://www.openssh.com/
You can do a remote and secure login to
your PC using ssh, and from a Windows machine using the program Putty
http://www.chiark.greenend.org.uk/sgtatham/putty/ , also make secure copies with scp.
GNU wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive command line tool, so it may easily be called from scripts, cron jobs, terminals without Xsupport, etc.
http://www.gnu.org/software/wget/wget.html
As an little example if you want to have
a local mirror of a web site you can do bash$ wget -m http://web
site
OpenOffice.org is the open source project through which Sun Microsystems has released the technology for the popular StarOffice[tm] Productivity Suite, with compatibility with MS Office, so you can read and write Win9x, W2000, XP MS Word, Excel and Power Point but also StarWritter,RTF and html. Now with medical terminology spell checker.
Open Office home page at http://www.openoffice.org/