Hello,

I am trying to run image registration following the adapted instructions provided below. I adjusted the registration parameters following (Randlett et al 2015) and this is the output I receive. It generates a "registration" folder containing an "affine" subfolder but the only contents of the subfolder are the cmd.sh command for the image to be registered. Thank you for the help! 


C:\Users\danah>cd C:\Users\danah\CMTKregistration\CMTKreg

C:\Users\danah\CMTKregistration\CMTKreg>perl C:\Users\danah\CMTKregistration\CMTK\bin\munger -b C:\Users\danah\CMTKregistration\CMTK\bin -a -w -r 01 -X52 -C8 -G80 -R3 -A "--accuracy 0.4" -W "--accuracy 1.6" -s template/template_01.nrrd images
hostname = DESKTOP-J8LE56N; short hostname = DESKTOP-J8LE56N
JOB ID =
Root directory is C:\Users\danah\CMTKregistration\CMTKreg
Changing to root directory: C:\Users\danah\CMTKregistration\CMTKreg
Setting image root to: images
MYEXEC: CMD = md Registration\affine\template_image_01_9dof.list exited with value 0
Aff:image_01 WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
MYEXEC: CMD = C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_image_01_9dof.list template/template_01.nrrd images/image_01.nrrd exited with value 255
Aff:image_01 WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
MYEXEC: CMD = C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_image_01_9dof.list template/template_01.nrrd images/image_01.nrrd exited with value 255
Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 2 failed
Ran 0 warp registrations
Reformatted 0 images

Dear Dana,

Unfortunately, I think we need a bit more information here.

Can you try inserting

-v

(verbose) in your munger command line? It could go here for example

-v -a -w

All the best,

Greg.


Originally posted by Dana Hodorovich:

> I think maybe the problem is the double quotes here - "--accuracy 0.4" -W
> "--accuracy 1.6"
>

Try with single quotation marks. I hand had issues with the quotes
before...

>

Hello,

This is the output I get when including the verbose command is as follows: 



C:\Users\danah\CMTKregistration\CMTKreg>perl "C:\Users\danah\CMTKregistration\CMTK\bin\munger" -b "C:\Users\danah\CMTKregistration\CMTK\bin" -v -a -w -r 0102 -T8 -X52 -C8 -G80 -R3 -A "--accuracy 0.4" -W "--accuracy 1.6" -s "template/template.nrrd" "images"
hostname = DESKTOP-J8LE56N; short hostname = DESKTOP-J8LE56N
User path is C:\Perl64\site\bin;C:\Perl64\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\NVIDIA Corporation\NVIDIA NvDLISR;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files\MATLAB\R2019a\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Program Files\SASHome\SASFoundation\9.4\core\sasexe;C:\Program Files\SASHome\SASFoundation\9.4\ets\sasexe;C:\Program Files\SASHome\Secure\ccme4;C:\Program Files\SASHome\x86\Secure\ccme4;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Users\danah\AppData\Local\Microsoft\WindowsApps;;C:\Users\danah\AppData\Local\Programs\Microsoft VS Code\bin
Reference brain is template/template.nrrd
Reference brain stem is template
JOB ID =
Start time is: 1595861380 seconds
Root directory is C:\Users\danah\CMTKregistration\CMTKreg
Changing to root directory: C:\Users\danah\CMTKregistration\CMTKreg
Setting image root to: images
Found brain name TLF_ 01 (images/TLF_01.nrrd)
New working directory is: C:\Users\danah\CMTKregistration\CMTKreg, Old one was C:/Users/danah/CMTKregistration/CMTKreg/images
MYEXEC: CMD = md Registration\affine\template_TLF_01_9dof.list exited with value 0
A: Running affine reg with command: C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd
INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
MYEXEC: CMD = C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd exited with value 255
inlist = Registration\affine\template_TLF_01_9dof.list
W: outlist = Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Reformat:inlist would be: Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Found brain name TLF_ 02 (images/TLF_02.nrrd)
New working directory is: C:\Users\danah\CMTKregistration\CMTKreg, Old one was C:/Users/danah/CMTKregistration/CMTKreg/images
Reformat:inlist would be: Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
-------------------------
Rescanning images directory a second time
-------------------------
Found brain name TLF_ 01 (images/TLF_01.nrrd)
New working directory is: C:\Users\danah\CMTKregistration\CMTKreg, Old one was C:/Users/danah/CMTKregistration/CMTKreg/images
A: Running affine reg with command: C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd
INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
MYEXEC: CMD = C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd exited with value 255
inlist = Registration\affine\template_TLF_01_9dof.list
W: outlist = Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Reformat:inlist would be: Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Found brain name TLF_ 02 (images/TLF_02.nrrd)
New working directory is: C:\Users\danah\CMTKregistration\CMTKreg, Old one was C:/Users/danah/CMTKregistration/CMTKreg/images
Reformat:inlist would be: Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 2 failed
Ran 0 warp registrations
Reformatted 0 images

Thank you!

Dana

Originally posted by Owen Randlett: Hello Dr. Randlett,

When I replace the double quotations this is the output I receive:

C:\Users\danah\CMTKregistration\CMTKreg>perl "C:\Users\danah\CMTKregistration\CMTK\bin\munger" -b "C:\Users\danah\CMTKregistration\CMTK\bin" -v -a -w -r 0102 -T8 -X52 -C8 -G80 -R3 -A '--accuracy 0.4' -W '--accuracy 1.6' -s "template/template.nrrd" "images"
hostname = DESKTOP-J8LE56N; short hostname = DESKTOP-J8LE56N
User path is C:\Perl64\site\bin;C:\Perl64\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\NVIDIA Corporation\NVIDIA NvDLISR;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files\MATLAB\R2019a\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Program Files\SASHome\SASFoundation\9.4\core\sasexe;C:\Program Files\SASHome\SASFoundation\9.4\ets\sasexe;C:\Program Files\SASHome\Secure\ccme4;C:\Program Files\SASHome\x86\Secure\ccme4;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Users\danah\AppData\Local\Microsoft\WindowsApps;;C:\Users\danah\AppData\Local\Programs\Microsoft VS Code\bin
Reference brain is
Unable to read reference brain at C:\Users\danah\CMTKregistration\CMTK\bin\munger line 96.

Best,
Dana

Hi Dana,

Can you try running the command that’s failing manually?

You need to change to your CMTKreg folder.

Then eg

C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_TLF_01_9dof.list template/template.nrrd images/

And see what happens. I’m not sure about the mix of forwards and backwards slashes.

Best,

Greg.

Hi Greg,

When I manually run the command as you suggested, the only output I get is an error saying "ERROR: unidentified format of file images".. however when I specify the image name in the path, in this case it would be "template/template.nrrd" "images/TLF_01.nrrd", it will run and I only receive a warning about image orientation. But there is no additional output, just the original affine subfolder it created. I apologize for this going back and forth trying to pinpoint the issue. I truly appreciate your help!
Originally posted by Greg Jefferis:

Hi Dana,

When you do that test run from what I can see it’s reading in the two input images and then failing. Do you know if it’s failing immediately or is it spending some time doing some computation first? Does it really print nothing else to the screen?

Can you

1.send the screen output of the whole test run
2. Try the test run but swap the orientation of the slashes in the output location (see below)
3. Give a full recursive listing of the CMTKreg folder with

ls -lR

(or whatever the equivalent is in your shell eg dir rather than ls) so that we can see the permissions on all the folders
4. Tell us more about what (windows) platform you’re running on and how you installed cmtk.
5. If the above does not clarify can you put a complete zipped sample directory with the template and one input in the images folder and the commands folder and your output Registration folder after running the test online somewhere (you can share privately with me if you prefer)

Some possible sample hypotheses about what is happening

0. I don’t know what windows/shell etc flavour you are using but it doesn’t like the backslashes in the output path for your .list folder
1. The second image file is corrupt part way through
2. You have an unusual write permissions error on your folder
3. Your cmtk installation is partly corrupt eg there is a missing library but other parts still work

All the best,

Greg.


> C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd

Hi Greg,

My apologies, I responded to this post through my email on Friday and it didn't send. 

The test run from the manual registration line fails within 5-7 seconds. It will print the two warnings and that is it. Attached below is the entire output when I run the initial registration, and then manually enter the registration line with the orientation changed of the backslashes in the output location. I then included the "dir /s" of my CMTKreg folder. I am using a Windows environment through Active Perl. I followed the adapted instructions that I have attached.

C:\Users\danah\OneDrive\Documents>cd "C:\Users\danah\CMTKregistration\CMTKreg"
C:\Users\danah\CMTKregistration\CMTKreg>perl "C:\Users\danah\CMTKregistration\CMTK\bin\munger" -b "C:\Users\danah\CMTKregistration\CMTK\bin" -v -a -w -r 0102 -T8 -X52 -C8 -G80 -R3 -A "--accuracy 0.4" -W "--accuracy 1.6" -s "template/template.nrrd" "images"
hostname = DESKTOP-J8LE56N; short hostname = DESKTOP-J8LE56N
User path is C:\Perl64\site\bin;C:\Perl64\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\NVIDIA Corporation\NVIDIA NvDLISR;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files\MATLAB\R2019a\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Program Files\SASHome\SASFoundation\9.4\core\sasexe;C:\Program Files\SASHome\SASFoundation\9.4\ets\sasexe;C:\Program Files\SASHome\Secure\ccme4;C:\Program Files\SASHome\x86\Secure\ccme4;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Users\danah\AppData\Local\Microsoft\WindowsApps;;C:\Users\danah\AppData\Local\Programs\Microsoft VS Code\bin
Reference brain is template/template.nrrd
Reference brain stem is template
JOB ID =
Start time is: 1596046150 seconds
Root directory is C:\Users\danah\CMTKregistration\CMTKreg
Changing to root directory: C:\Users\danah\CMTKregistration\CMTKreg
Setting image root to: images
Found brain name TLF_ 01 (images/TLF_01.nrrd)
New working directory is: C:\Users\danah\CMTKregistration\CMTKreg, Old one was C:/Users/danah/CMTKregistration/CMTKreg/images
MYEXEC: CMD = md Registration\affine\template_TLF_01_9dof.list exited with value 0
A: Running affine reg with command: C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd
INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
MYEXEC: CMD = C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd exited with value 255
inlist = Registration\affine\template_TLF_01_9dof.list
W: outlist = Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Reformat:inlist would be: Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Found brain name TLF_ 02 (images/TLF_02.nrrd)
New working directory is: C:\Users\danah\CMTKregistration\CMTKreg, Old one was C:/Users/danah/CMTKregistration/CMTKreg/images
Reformat:inlist would be: Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
-------------------------
Rescanning images directory a second time
-------------------------
Found brain name TLF_ 01 (images/TLF_01.nrrd)
New working directory is: C:\Users\danah\CMTKregistration\CMTKreg, Old one was C:/Users/danah/CMTKregistration/CMTKreg/images
A: Running affine reg with command: C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd
INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
MYEXEC: CMD = C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd exited with value 255
inlist = Registration\affine\template_TLF_01_9dof.list
W: outlist = Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Reformat:inlist would be: Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Found brain name TLF_ 02 (images/TLF_02.nrrd)
New working directory is: C:\Users\danah\CMTKregistration\CMTKreg, Old one was C:/Users/danah/CMTKregistration/CMTKreg/images
Reformat:inlist would be: Registration\warp\template_TLF_01_warp_m0g80c8e1e-1x52r3.list
Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 2 failed
Ran 0 warp registrations
Reformatted 0 images
C:\Users\danah\CMTKregistration\CMTKreg>C:\Users\danah\CMTKregistration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/template_TLF_01_9dof.list template/template.nrrd images/TLF_01.nrrd
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
C:\Users\danah\CMTKregistration\CMTKreg>dir /s
Volume in drive C is OS
Volume Serial Number is B079-96D8
Directory of C:\Users\danah\CMTKregistration\CMTKreg
07/29/2020 02:09 PM .
07/29/2020 02:09 PM ..
07/23/2020 10:10 AM command
07/27/2020 03:28 PM images
07/29/2020 02:09 PM Registration
07/27/2020 10:20 AM template
0 File(s) 0 bytes
Directory of C:\Users\danah\CMTKregistration\CMTKreg\command
07/23/2020 10:10 AM .
07/23/2020 10:10 AM ..
07/27/2020 03:04 PM 197 reformat.cmd.cmd
07/27/2020 03:47 PM 260 registration.cmd.cmd
2 File(s) 457 bytes
Directory of C:\Users\danah\CMTKregistration\CMTKreg\images
07/27/2020 03:28 PM .
07/27/2020 03:28 PM ..
07/27/2020 03:44 PM 1,017,446,680 TLF_01.nrrd
07/27/2020 03:45 PM 1,017,446,680 TLF_02.nrrd
2 File(s) 2,034,893,360 bytes
Directory of C:\Users\danah\CMTKregistration\CMTKreg\Registration
07/29/2020 02:09 PM .
07/29/2020 02:09 PM ..
07/29/2020 02:09 PM affine
0 File(s) 0 bytes
Directory of C:\Users\danah\CMTKregistration\CMTKreg\Registration\affine
07/29/2020 02:09 PM .
07/29/2020 02:09 PM ..
07/29/2020 02:09 PM template_TLF_01_9dof.list
0 File(s) 0 bytes
Directory of C:\Users\danah\CMTKregistration\CMTKreg\Registration\affine\template_TLF_01_9dof.list
07/29/2020 02:09 PM .
07/29/2020 02:09 PM ..
07/29/2020 02:09 PM 199 cmd.sh
1 File(s) 199 bytes
Directory of C:\Users\danah\CMTKregistration\CMTKreg\template
07/27/2020 10:20 AM .
07/27/2020 10:20 AM ..
07/27/2020 03:44 PM 240,983,055 template.nrrd
1 File(s) 240,983,055 bytes
Total Files Listed:
6 File(s) 2,275,877,071 bytes
20 Dir(s) 380,691,398,656 bytes freeOriginally posted by Greg Jefferis:

My only other suggestion at this point is to share sample data off list as I can’t see any clues in what you’ve sent.

Hi Greg,

Would you mind emailing me (drhodoro@ncsu.edu) so I can share the compressed folder with you? Thank you.