Hey all,
I am struggling with the CMTK tool for a few days now. I finally got it running, however, the registration always fails to execute and it tells me "no such file or directory". I found a post from March 13, 2017, where exactly the same problem was described. However, no solution was suggested (or maybe I missed it).

The generated script is:

hostname = sarah-pc; short hostname = sarah-pc
JOB ID =
Root directory is /home/sarah/yourregistrationfolder
Changing to root directory: /home/sarah/yourregistrationfolder
Setting image root to: images
Aff:21OctSP8Fish1_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish1_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish1_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish3_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish3_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish3_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish4_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish4_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish4_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish2_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish2_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish2_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish1_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish1_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish1_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish3_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish3_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish3_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish4_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish4_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish4_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish2_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish2_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish2_01.nrrd failed to execute: No such file or directory

Ran 0 initial affine registrations of which 0 failed
Ran 8 affine registrations of which 8 failed
Ran 0 warp registrations
Reformatted 0 images

As suggested in the 2017 post, I have already checked with ls and all the nrrd files are where they are supposed to be...

I also have one additional question: I have 2 channels, one for tERK and one for pERK. Does it matter which one is 01 and which one is 02?

Best,
Sarah

Hi Sarah,

First of all, what platform are you on? 

For the missing files, I suggest you do the following.

Go to your terminal command line application (Cygwin?)

to see if we can figure out which file is missing.

Re this question:
It is a bit easier if the reference channel for registration is channel 01. If your reference channel is channel 02, you need add an extra command line option to inform the tools about this.

All the best,

Greg.

Hi Greg,

Thank you for your fast response. I am using Manjaro in a virtual box...

As you suggested I checked which files are missing:

ls refbrain/Ref20131120pt14pl2.nrrd I can find the refbrain

ls images/21OctSP8Fish1_01.nrrd I can find all the images

ls /home/sarah/Fiji.app/bin/cmtk/bin/registration I cannot find registration in the cmtk bin.


Maybe I mixed up the folder structure when I installed CMTK (not with Fiji). The folder structure currently looks like this:

/home/sarah/Fiji.app/bin/cmtk/

In the cmtk folder are four subfolders (bin, include, lib and share)

/home/sarah/Fiji.app/bin/cmtk/bin/ includes the cmtk and munger script.

There is a folder which is called Registration, however, it is not in the bin..it is included in the following folders

/home/sarah/Fiji.app/bin/cmtk/include/cmtk/Registration

Is this the folder I was looking for with ls /home/sarah/Fiji.app/bin/cmtk/bin/registration ? Do I need to move it somewhere else?

Cheers,
Sarah

Hi Sarah,

The problem is that you either need to install cmtk from inside Fiji *or* edit the shell scripts to point at your external CMTK installation.

To instal from within Fiji follow the menu item to install cmtk under Plugins CMTK gui.

Best,

Greg.

Hi Greg,

I have now installed CMTK from inside Fiji. The problem is that the folder /home/sarah/Fiji.app/bin/cmtk does not contain anything. So the scripts etc are missing...

This is why I installed CMTK without Fiji and added the scripts to the respective folders. I think I need to go for your suggestion with editing the shell scripts then :-/

Cheers,
Sarah

It sounds like the install cannot have finished properly.

Can you send me offline what you get by running

ls -R /home/sarah/Fiji.app/bin/

Editing the scripts is not complicated so long as we know where the cmtk stuff lives. Can you post a sample script? Can you also try doing:

which cmtk
which registrationx

To confirm the binary location.

All the best,

Greg.

Dear Greg,
I have a similar issue here - i.e, no such file or directory. 
However, I am running CMTK registration GUI in FIJI, not terminal. What could have gone wrong in my case?
I tried to download the sample data from wiki but its no longer there.


Last login: Wed Feb 5 12:10:56 on ttys001
/Users/caroline/Desktop/yourregistrationfolder/commands/munger_2020-02-05_12.10.27.command ; exit;
m219010306:~ caroline$ /Users/caroline/Desktop/yourregistrationfolder/commands/munger_2020-02-05_12.10.27.command ; exit;
/Users/caroline/Desktop/yourregistrationfolder/commands/munger_2020-02-05_12.10.27.command: line 4: /Applications/Fiji.app/bin/cmtk/munger: No such file or directory
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.

[Process completed]


Cheers,
Caroline

Dear Caroline,

Please can you confirm that you have followed the instructions to install the cmtk software using this menu item:

Plugins>CMTK Registration>Install CMTK

If you have, then please say what error message it gives if it doesn’t work — it hasn’t completed properly.

I am sorry but you’re right that the institute data server that used to host the sample dataset has been retired. I’ll look for an alternative location.

Best,

Greg.

Hello,

Sorry to add to the confusion, but Im currently encountering a similar issue when trying to use the CMTK Registration GUI within Fiji on Ubuntu. I installed the CMTK GUI using the update site and used Plugins>CMTK Registration > Install CMTK  to install CMTK. This successfully generates a Fiji.app/bin/cmtk directory containing several files . However, within this directory, there is no bin directory ( I gather from this thread that there should be a bin/registration directory).
When I try to run the registration from the CMTK Gui, I get an error message that indicates there may be files missing from my CMTK directory:

Root directory is/home/isabel/Desktop/Registration
Aff:20190115_R26B07_MCFO_slide48_nc82 /home/isabel/Downlaods/Fiji.app/bin/cmtk/registration: error while loading shared libraries: libdcmdata.so.4: cannot open shared object file: No such file or directory
MYEXEC: CMD = /home/isabel/Downloads/Fiji.app/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/JFRC2010_20190115_R26B07_MCFO_slide48_nc82_9dof.list reference/JFRC2010_Mask.nrrd images 20190115_R26B07_MCFO_slide48_nc82.nrrd exited with value 127

Has anyone encountered this issue or know how to go about fixing this problem?
Thanks!
Isabel

Hi Isabel, look for instructions in recent past messages on the forum about compiling cmtk on Ubuntu. It looks like the precompiled binaries will not work on your platform. Best, Greg.

Hi Isabel,

More specifically please see this message for linux install information:

https://www.nitrc.org/forum/message.php?...

Best,

Greg.