I've had success running cmtk and munger commands locally on my mac, and am now trying to get it to work on a computing cluster running centos 7 (no root access). I built from source using directions in this forum:

• Download the source code into a convenient directory
• Unpack the archive: tar -xzvf CMTK-3.3.1-Source.tar.gz
• Make and change into a build directory: mkdir build; cd build
• Configure CMTK (including optimizations for x86_64 CPUs): cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_TESTING=OFF -D BUILD_CONTRIB=ON -D BUILD_CONTRIB_MUNGER=ON -C ../cmtk-3.1.1/config/gcc-x86_64-sse.cmake ../cmtk-3.3.1
• Run build: make -j4

I used cmake/3.11.1
I also added the /bin directory to my path in .bash_profile

When I run:
munger -a -w -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 2 -s Meanbrain.nii Template.nii

I get this output:
hostname = sh-107-33.int; short hostname = sh-107-33.int
JOB ID =
Root directory is /home/users/brezovec/temp
MYEXEC: CMD = mkdir -p Registration/affine/Meanbrain_Template.nii_9dof.list exited with value 0
Aff:Template.nii INFO: number of threads set to 2 according to environment variable CMTK_NUM_THREADS
Entering resolution level 1 out of 4...
Entering resolution level 1 out of 4...
Entering resolution level 2 out of 4...
Entering resolution level 2 out of 4...
Entering resolution level 3 out of 4...
Entering resolution level 3 out of 4...
Entering resolution level 4 out of 4...
Entering resolution level 4 out of 4...
Resulting transformation parameters:
#0d: 2.693778
#1d: 12.293778
#2d: 27.385254
#3d: 18.609026
#4d: -1.292293
#5d: 0.612162
#6d: 0.977335
#7d: 1.069253
#8d: 1.698828
#9d: 0.000000
#10d: 0.000000
#11d: 0.000000
#12d: 158.943488
#13d: 158.943488
#14d: 67.496550
MYEXEC: CMD = /home/users/brezovec/cmtk/build/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Meanbrain_Template.nii_9dof.list Meanbrain.nii Template.nii exited with value 0
MYEXEC: CMD = mkdir -p "Registration/warp/Meanbrain_Template.nii_warp_m0g80c8e1e-1x26r4.list" exited with value 0
Warp Template.nii,INFO: number of threads set to 2 according to environment variable CMTK_NUM_THREADS
WARNING: the following command line arguments were not used:
0.4 -o Registration/warp/Meanbrain_Template.nii_warp_m0g80c8e1e-1x26r4.list Registration/affine/Meanbrain_Template.nii_9dof.list
Unknown option: -c [argument #0]
MYEXEC: CMD = /home/users/brezovec/cmtk/build/bin/warp -v --registration-metric nmi --jacobian-weight 0 --fast -e 26 --grid-spacing 80 --energy-weight 1e-1 --refine 4 --coarsest 8 --ic-weight 0 --output-intermediate -accuracy 0.4 -o Registration/warp/Meanbrain_Template.nii_warp_m0g80c8e1e-1x26r4.list Registration/affine/Meanbrain_Template.nii_9dof.list exited with value 1

I don't understand this unknown option error.

For comparison, when I run this command on my mac, this is the output:
hostname = Luke; short hostname = Luke
JOB ID =
Root directory is /Users/lukebrezovec/cmtk_tests/20191201
MYEXEC: CMD = mkdir -p Registration/affine/Meanbrain_Template.nii_9dof.list exited with value 0
Aff:Template.nii INFO: number of threads set to 2 according to environment variable CMTK_NUM_THREADS
Entering resolution level 1 out of 4...
Entering resolution level 1 out of 4...
Entering resolution level 2 out of 4...
Entering resolution level 2 out of 4...
Entering resolution level 3 out of 4...
Entering resolution level 3 out of 4...
Entering resolution level 4 out of 4...
Entering resolution level 4 out of 4...
Resulting transformation parameters:
#0d: -8.800000
#1d: 50.895430
#2d: -17.800000
#3d: -0.797136
#4d: -1.544450
#5d: 3.220954
#6d: 0.842525
#7d: 1.140147
#8d: 1.506569
#9d: 0.000000
#10d: 0.000000
#11d: 0.000000
#12d: 196.221976
#13d: 140.926547
#14d: 125.000000
MYEXEC: CMD = /opt/local/lib/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Meanbrain_Template.nii_9dof.list Meanbrain.nii Template.nii exited with value 0
MYEXEC: CMD = mkdir -p "Registration/warp/Meanbrain_Template.nii_warp_m0g80c8e1e-1x26r4.list" exited with value 0
Warp Template.nii,INFO: number of threads set to 2 according to environment variable CMTK_NUM_THREADS
Reading input studylist Registration/affine/Meanbrain_Template.nii_9dof.list
Entering resolution level 1 out of 4...
Setting step size to 25.6 [mm]
Deactivated 27 out of 756 parameters.
Setting step size to 12.8 [mm]
Setting step size to 6.4 [mm]
Setting step size to 3.2 [mm]
Setting step size to 1.6 [mm]
Setting step size to 0.8 [mm]
Setting step size to 0.4 [mm]
Entering resolution level 2 out of 4...
Setting step size to 12.8 [mm]
Deactivated 996 out of 2673 parameters.
Setting step size to 6.4 [mm]
Setting step size to 3.2 [mm]
Setting step size to 1.6 [mm]
Setting step size to 0.8 [mm]
Setting step size to 0.4 [mm]
Entering resolution level 3 out of 4...
Setting step size to 6.4 [mm]
Deactivated 7497 out of 12825 parameters.
Setting step size to 3.2 [mm]
Setting step size to 1.6 [mm]
Setting step size to 0.8 [mm]
etc.....

Thank you very much for your help!

Hi Luke,

It seems that something funny is happening with the second —accuracy option. It is written as -accuracy (ie one dash not two). This would be interpreted as passing the -a -c etc arguments to minger. I’m not sure if this is a funny quoting error or just a typo in your command line. If it’s not a typo maybe try running

> munger -a -w -X 26 -C 8 -G 80 -R 4 -T 2 -s Meanbrain.nii Template.nii

and see if that works. All the best,

Greg.

Hi Greg,

Good eye! That was it - thanks a lot!

Best,
Luke