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