Opening DICOM File Format images in Debian
Testing/Unstable with MRICRON
Digital Imaging and Communications in Medicine is a well
established standard for handling storing, printing and
transmitting information in medical imaging.
I've recently been through a
RMI
Scan
The image in the beginning of the blog post is actually the RMI
scan of my brain :)!
The Doctors which took participation in the Magnetic Resonance
Examination gave me a whole CD with pictures of my brain in the
DICOM file format. Though the CD I was provided
with included a Windows version of a program called
Dicom
Viewer I didn't have a way to open the DICOM file format on my
Debian Linux
A quick research in Google indicated that happily the
DICOM file
format is able to be opened also in GNU/Linux
There are few options if you'd like to open the file format on
Linux.
The easiest one seemed through
the KDE's Kradview DICOM
opening application. Kradview is quite simple, it is created
for just one purpose opening DICOM file format on Linux, nothing
more or less. So don't expect too much!
Kradview didn't have a precompiled package for the Debian Linux
distrubution, that's why if you indend to use this software on
Debian Linux you'll have to compile it from source as explained on
Kradview's website
Install instructions
I am naturally a Gnome user and therefore Kradview was not
something that fits my Gnome taste. Trying to compile it on my
gnome ended with the nasty compile time error:
checking for Qt... configure: error: Qt (>= Qt 3.0)
(headers and libraries) not found. Please check your installation!
For more details about this problem, look at the end of
config.log.
Definitely not cool, thefore I was forced
to look for some alternatives to Kradview which will either be
easily compiled and installed from source on Debian or even better
will be prepackaged in the debian's deb file format.
A quick search led me to the
Debian's Neuro Science
Repository!
Truly I never suspected Debian is SO BIG! This guys even have a
separate repository for neuro science, that's wild seriously!
Quick look through Debia's neuro science repository led me to a
nifty software called
MRICron
MRICron is a package which includes few gui based
executables which are capable of:
magnetic resonance image conversion, viewing and
analysis
quite cool!
There was even a package for sid which good suited me since my
Desktop is running on top of Debian Testing Unstable.
I used the
Following
repository link to download the Debian Sid testing/unstable MRICron
package
I'm running a 64 bit debian (amd64) therefore I needed to download
and install the 64 bit release of MRICron.
Here is how I did it:
hipo@noah:~# wget
http://neuro.debian.net/debian/pool/main/m/mricron/mricron-data_0.20100422.1~dfsg.1-1~sid.nd1_all.deb
hipo@noah:~# wget
http://neuro.debian.net/debian/pool/main/m/mricron/mricron_0.20100422.1~dfsg.1-1~sid.nd1_amd64.deb
Then I used Debian's dpkg to install the packages, as you can see
down:
hipo@noah:~# dpkg -i
mricron-data_0.20100422.1~dfsg.1-1~sid.nd1_all.deb
hipo@noah:~# dpkg -i
mricron_0.20100422.1~dfsg.1-1~sid.nd1_amd64.deb
I was lucky that I had all the dependcy packages required by
mricron-data and the mricron debian sid packages. And the two ones
installed "in a blink of an eye without no further issues".
As I already had the mricron installed I had to invoke from command
line the:
hipo@noah:~# /usr/bin/dcm2niigui
I used the dcm2niigui selecting the DICOM medical imaging data
files to convert them to
the Nifty file format (*.nii)
Next I used the
hipoa@noah:~#
/usr/bin/mricron
to open the converted DICOM format files to the Nifty Format. I
won't sink into details about how to use the two forementioned
problems since their user interface is quite
self-explanatory.
The results from the RMI scan examinations prooved my fears that I
could be suffering a severe brian damage completely
groundless.
Praise the Lord for that!
In another post I'll sink into details on what kind of thought
tortures I've been through before the RMI examination showed I
don't have problems with my brian.
Here is one more wondeful looking picture from above taken by the
RMI machine during the RMI examinations.
I'm really happy that Linux is developing day by day and that I
could see the DICOM pictures of my brain even on a free software
platform as Linux is!