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users > RE: Unable to read reference image
Mar 20, 2017 06:03 PM | Dan Xie - UCSF
RE: Unable to read reference image
Hi Torsten,
Thank you so much for spending time to rebuild the package! I appreciate your help. Now the incompatibility disappears, but the package cannot find my data files.
My working folder is: D:\Data\cmtkRegistration
which originally contains three folders:
D:\Data\cmtkRegistration\commands (generated by CMTK GUI)
D:\Data\cmtkRegistration\images (created by me, contains two image stacks FBZD01.nrrd, FBZD02.nrrd)
D:\Data\cmtkRegistration\refbrain (created by me, contains one reference image Nov012016B3ZDref.nrrd)
Since my FIJI cmtk plugin fails, I manually changed the paths of munger and cmtk in a previous munger script, so the script becomes:
#!/bin/sh
# 2017-03-14_10.13.30
cd "D:\Data\cmtkRegistration"
"C:\cygwin64\usr\local\bin\munger" -b "C:\cygwin64\usr\local\bin\cmtk" -a -w -r 010203 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 1 -s "refbrain\Nov012016B3ZDref.nrrd" images
Running the munger script yields the error message:
$ sh munger_2017-03-14_10.13.30.sh
hostname = Admin-PC; short hostname = Admin-PC
JOB ID =
Root directory is /d/Data/cmtkRegistration
Changing to root directory: /d/Data/cmtkRegistration
Setting image root to: images
Aff:FBZD01 MYEXEC: CMD = C:/cygwin64/usr/local/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/refbrain/Nov012016B3ZDref_FBZD01_9dof.list refbrain\Nov012016B3ZDref.nrrd images/FBZD01.nrrd failed to execute: No such file or directory
Aff:FBZD01 MYEXEC: CMD = C:/cygwin64/usr/local/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/refbrain/Nov012016B3ZDref_FBZD01_9dof.list refbrain\Nov012016B3ZDref.nrrd images/FBZD01.nrrd failed to execute: No such file or directory
Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 2 failed
Ran 0 warp registrations
Reformatted 0 images
The "Registration" folder is created upon the execution, which means it can recognize my working folder. However, the program insists that my image files don't exist. Do you have any idea what went wrong?
Best,
Dan
Thank you so much for spending time to rebuild the package! I appreciate your help. Now the incompatibility disappears, but the package cannot find my data files.
My working folder is: D:\Data\cmtkRegistration
which originally contains three folders:
D:\Data\cmtkRegistration\commands (generated by CMTK GUI)
D:\Data\cmtkRegistration\images (created by me, contains two image stacks FBZD01.nrrd, FBZD02.nrrd)
D:\Data\cmtkRegistration\refbrain (created by me, contains one reference image Nov012016B3ZDref.nrrd)
Since my FIJI cmtk plugin fails, I manually changed the paths of munger and cmtk in a previous munger script, so the script becomes:
#!/bin/sh
# 2017-03-14_10.13.30
cd "D:\Data\cmtkRegistration"
"C:\cygwin64\usr\local\bin\munger" -b "C:\cygwin64\usr\local\bin\cmtk" -a -w -r 010203 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 1 -s "refbrain\Nov012016B3ZDref.nrrd" images
Running the munger script yields the error message:
$ sh munger_2017-03-14_10.13.30.sh
hostname = Admin-PC; short hostname = Admin-PC
JOB ID =
Root directory is /d/Data/cmtkRegistration
Changing to root directory: /d/Data/cmtkRegistration
Setting image root to: images
Aff:FBZD01 MYEXEC: CMD = C:/cygwin64/usr/local/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/refbrain/Nov012016B3ZDref_FBZD01_9dof.list refbrain\Nov012016B3ZDref.nrrd images/FBZD01.nrrd failed to execute: No such file or directory
Aff:FBZD01 MYEXEC: CMD = C:/cygwin64/usr/local/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/refbrain/Nov012016B3ZDref_FBZD01_9dof.list refbrain\Nov012016B3ZDref.nrrd images/FBZD01.nrrd failed to execute: No such file or directory
Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 2 failed
Ran 0 warp registrations
Reformatted 0 images
The "Registration" folder is created upon the execution, which means it can recognize my working folder. However, the program insists that my image files don't exist. Do you have any idea what went wrong?
Best,
Dan
Threaded View
Title | Author | Date |
---|---|---|
Dan Xie | Mar 13, 2017 | |
Greg Jefferis | Mar 13, 2017 | |
Dan Xie | Mar 13, 2017 | |
Greg Jefferis | Mar 14, 2017 | |
Torsten Rohlfing | Mar 14, 2017 | |
Dan Xie | Mar 14, 2017 | |
Torsten Rohlfing | Mar 15, 2017 | |
Dan Xie | Mar 20, 2017 | |
Greg Jefferis | Mar 20, 2017 | |
Dan Xie | Mar 20, 2017 | |
Greg Jefferis | Mar 14, 2017 | |
Dan Xie | Mar 14, 2017 | |