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users > RE: CMTK failing after affine registration
Aug 2, 2020 02:08 PM | Dana Hodorovich - North Carolina State University
RE: CMTK failing after affine registration
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 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:
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
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
Threaded View
| Title | Author | Date |
|---|---|---|
| Dana Hodorovich | Jul 26, 2020 | |
| Owen Randlett | Jul 26, 2020 | |
| Dana Hodorovich | Jul 27, 2020 | |
| Greg Jefferis | Jul 26, 2020 | |
| Dana Hodorovich | Jul 27, 2020 | |
| Greg Jefferis | Jul 27, 2020 | |
| Dana Hodorovich | Jul 27, 2020 | |
| Greg Jefferis | Jul 28, 2020 | |
| Dana Hodorovich | Aug 2, 2020 | |
| Greg Jefferis | Aug 2, 2020 | |
| Dana Hodorovich | Aug 2, 2020 | |