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Jun 13, 2017  06:06 AM | Maggie Yan
CMTK installation in Linux system
Hello, I downloaded CMTK-3.3.1-Linux-x86_64.tar.gz and wanted to install it in my Linux system. Also, I downloaded UserGuideCMTK.pdf. But I could't find relative information to instruct me in installation. Would you like to tell me how can I install CMTK in my computor and how to validate that I install it successfully? Hope to get your reply soon, thanks very much!
Jun 13, 2017  03:06 PM | Greg Jefferis
CMTK installation in Linux system
You can untar the file using the Linux terminal. I guess there is a way to expand using a gui tool as well. Then you need to make sure that the directory containing the binaries is in your path. This is pretty typical for many software binary distributions, so googling should give you some examples you could adapt. You may also want to try the rpm file depending which Linux distribution you are running. This will likely take care of putting the files in a standard location.


Jun 14, 2017  01:06 AM | Greg Jefferis
CMTK installation in Linux system
On a red hat based system (e.g. centos/scientific linux/suse) you should be able to double click the CMTK-3.3.1-Linux-x86_64-core.rpm in your desktop – then it should fire up the package manager and offer to install.

You can install cmtk on debian based linux systems (e.g. Ubuntu) using a package manager by making use of the neurodebian distribution. Instructions here:

http://neuro.debian.net/install_pkg.html...

Best,

Greg.

Jun 14, 2017  07:06 PM | Torsten Rohlfing - Google LLC
RE: CMTK installation in Linux system
Originally posted by Greg Jefferis:
You can untar the file using the Linux terminal. I guess there is a way to expand using a gui tool as well. Then you need to make sure that the directory containing the binaries is in your path. This is pretty typical for many software binary distributions, so googling should give you some examples you could adapt. You may also want to try the rpm file depending which Linux distribution you are running. This will likely take care of putting the files in a standard location.



Just to add some detail to Greg's response -

The RPM will install CMTK under /usr/local. Specifically, the "cmtk" and "munger" wrapper scripts will be found in /usr/local/bin; if you add that to your path (if it's not there already), then you will be able to call all CMTK command line tools and helper scripts via

cmtk TOOL ARGS

where "TOOL" is the name of the tool (e.g., "registrationx"), and "ARGS" would be any arguments to the tool, command line options, etc.

The tools and executable scripts themselves, however, would be in /usr/local/lib/cmtk/bin/ - so if you wanted to call tools directly, without the wrapper script, then you'd need that in your path as well (or give absolute path every time you run a command).

Hope this helps.

Torsten
Jul 20, 2017  11:07 PM | Erin Wang
RE: CMTK installation in Linux system
Hi Greg,

I tried installing the CMTK rpm from my desktop, but it gave the following errors:
cmtk-core-3.3.1-1.x86_64 requires libdcmjpeg.so.4()(64bit)
cmtk-core-3.3.1-1.x86_64 requires liboflog.so.4()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libc.so.6(GLIBC_2.14)(64bit)
cmtk-core-3.3.1-1.x86_64 requires libijg12.so.4()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libstdc++.so.6(GLIBCXX_3.4.21)(64bit)
cmtk-core-3.3.1-1.x86_64 requires libpng16.so.16()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libdcmimage.so.4()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libtiff.so.5()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libijg16.so.4()(64bit)
cmtk-core-3.3.1-1.x86_64 requires dcmtk >= 3.5.4
cmtk-core-3.3.1-1.x86_64 requires libdcmdata.so.4()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libijg8.so.4()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libfftw3_omp.so.3()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libdcmimgle.so.4()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libofstd.so.4()(64bit)
cmtk-core-3.3.1-1.x86_64 requires libdcmjpls.so.4()(64bit)

Would you happen to know why this is happening?

Erin
Jul 22, 2017  04:07 PM | Torsten Rohlfing - Google LLC
RE: CMTK installation in Linux system
Hi Erin -

CMTK requires a few system and third-party packages to be installed in your system. What your seeing is the package installed telling you that it cannot satisfy these requirements.

Since the listed missing packages include the system C and C++ runtime libraries, this is very like the result of a version mismatch between the system on which the package was built (aka my home computer) and the system you're trying to install on.

I recall that I build the package on a Fedora 24 system, so hypothetically, on that version of that distribution, you should not be experiencing any problems. But that is hardly worth switching your OS for, so let's forget about that.

Sadly, since you have the system you have and I have the one I have, the simplest way to solve your problem would be to build CMTK from source code yourself.

It's not actually that hard, but you will need at least a C++ compiler (gcc recommended but clang should work) and CMake to be installed on your system.

Then follow these steps:

1. Download https://www.nitrc.org/frs/download.php/8... say into your home directory.
2. mkdir ~/cmtk
3. cd ~/cmtk
4. tar -xzvf ~/CMTK-3.3.1-Source.tar.gz
5. mkdir build
6. cd build
7. cmake -C ../core/config/gcc-x86_64-sse.cmake ../core/
8. make

After that you should find the CMTK binaries in the ~/cmtk/build/bin directory. If you want to properly install the package, you should be able to run the following to make an RPM package that is compatible with all the specific system library versions on your machine:

cpack -G RPM

Let me know if you run into problems.

Best,
  Torsten
Aug 21, 2017  12:08 PM | Elijah Rockers
RE: CMTK installation in Linux system
Worked like a charm on Centos 7, thank you.
Feb 28, 2018  10:02 AM | Greg Fleishman
RE: CMTK installation in Linux system
Building from source using Torsten's exact command sequence worked for me with one simple modification: I replaced "core" in both places with "cmtk-3.3.1" as this was the name of the decompressed source directory.

OS: Scientific Linux 7.4
cmake version: 2.8.12.2

I did this build and install in my home directory on a cluster, i.e. I don't have write permission for /usr/local/bin or similar OS directories. I added the absolute path to ~/cmtk/build/bin to my path:

cd ~/cmtk/build/bin
PATH=${PATH}:$( pwd )

and

cmtk --help
cmtk TOOL --help

seem to work fine. I've now added

PATH=${PATH}:/PATH/TO/CMTK/BINARIES

to my ~/.bashrc.