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users > Reformat script crashing
May 10, 2016 06:05 PM | Gabriella Sterne - Janelia Research Campus
Reformat script crashing
Hello,
This is my first time posting to the forum so please let me know if I have not provided sufficient information!
I am attempting to register Drosophila brain images to a template using nc82 staining. I would like to register 16-bit images. My system is 64-bit Windows 7 Professional. I set up CMTK using the following tutorial:
http://researchmap.jp/jo57feb6e-2041067/...
I am using ActivePerl 5.22.1 Build 2201 (64-bit) and CMTK-3.2.2-Windows-x86 and working with a 16-bit .PIC template as well as 16-bit .PIC images.
I am having two issues, which might be related or unrelated:
1) After running my registration file:
cd "C:\CMTKresults\CMTKreg
perl "C:\CMTKresults\CMTK\bin\munger" -b "C:\CMTKresults\CMTK\bin" -awr 01 -T 8 -s "template/template16.PIC" "images"
Everything appears to run smoothly. However, following the completion of the program I no longer get any file in the "reformatted" folder.
2) I previously was able to remedy this problem by running the following reformat script:
cd "C:\CMTKresults\CMTKreg"
perl "C:\CMTKresults\CMTK\bin\munger" -b "C:\CMTKresults\CMTK\bin" -r 01 -f 01 -T 8 -s "template/template16.PIC" "images"
which would then give me a reformatted .nrrd of the registered _01 image. However, recently, the above script fails. I receive a message from Windows saying "reformatx.exe has stopped working". If I view the problem details I see the following:
Problem signature:
Problem Event Name: APPCRASH
Application Name: reformatx.exe
Application Version: 0.0.0.0
Application Timestamp: 53dbd96b
Fault Module Name: MSVCR100.dll
Fault Module Version: 10.0.40219.1
Fault Module Timestamp: 4d5f0c22
Exception Code: 40000015
Exception Offset: 0008d6fd
OS Version: 6.1.7601.2.1.0.256.48
Locale ID: 1033
Additional Information 1: 6c7b
Additional Information 2: 6c7b33b39693521b9f38e6365f643500
Additional Information 3: 0510
Additional Information 4: 051044f64499f858b746874ce044c411
I have attempted to reinstall reformatx.exe and MSCVR100.dll with no change. If I say "close the program" the error message disappears but pops us a few more times before the program finally closes. If the check the "reformatted" folder, there are no images. In addition, changing the reformat script to:
cd "C:\CMTKresults\CMTKreg"
perl "C:\CMTKresults\CMTK\bin\munger" -b "C:\CMTKresults\CMTK\bin" -r 02 -f 01 -T 8 -s "template/template16.PIC" "images"
leads to identical results.
Interestingly, I am able to register 8-bit .PIC files to an 8-bit .PIC template without incident. Unfortunately I need to use 16-bit images.
Any suggestions would be greatly appreciated! My apologies if the solution is completely obvious.
Thank you!
This is my first time posting to the forum so please let me know if I have not provided sufficient information!
I am attempting to register Drosophila brain images to a template using nc82 staining. I would like to register 16-bit images. My system is 64-bit Windows 7 Professional. I set up CMTK using the following tutorial:
http://researchmap.jp/jo57feb6e-2041067/...
I am using ActivePerl 5.22.1 Build 2201 (64-bit) and CMTK-3.2.2-Windows-x86 and working with a 16-bit .PIC template as well as 16-bit .PIC images.
I am having two issues, which might be related or unrelated:
1) After running my registration file:
cd "C:\CMTKresults\CMTKreg
perl "C:\CMTKresults\CMTK\bin\munger" -b "C:\CMTKresults\CMTK\bin" -awr 01 -T 8 -s "template/template16.PIC" "images"
Everything appears to run smoothly. However, following the completion of the program I no longer get any file in the "reformatted" folder.
2) I previously was able to remedy this problem by running the following reformat script:
cd "C:\CMTKresults\CMTKreg"
perl "C:\CMTKresults\CMTK\bin\munger" -b "C:\CMTKresults\CMTK\bin" -r 01 -f 01 -T 8 -s "template/template16.PIC" "images"
which would then give me a reformatted .nrrd of the registered _01 image. However, recently, the above script fails. I receive a message from Windows saying "reformatx.exe has stopped working". If I view the problem details I see the following:
Problem signature:
Problem Event Name: APPCRASH
Application Name: reformatx.exe
Application Version: 0.0.0.0
Application Timestamp: 53dbd96b
Fault Module Name: MSVCR100.dll
Fault Module Version: 10.0.40219.1
Fault Module Timestamp: 4d5f0c22
Exception Code: 40000015
Exception Offset: 0008d6fd
OS Version: 6.1.7601.2.1.0.256.48
Locale ID: 1033
Additional Information 1: 6c7b
Additional Information 2: 6c7b33b39693521b9f38e6365f643500
Additional Information 3: 0510
Additional Information 4: 051044f64499f858b746874ce044c411
I have attempted to reinstall reformatx.exe and MSCVR100.dll with no change. If I say "close the program" the error message disappears but pops us a few more times before the program finally closes. If the check the "reformatted" folder, there are no images. In addition, changing the reformat script to:
cd "C:\CMTKresults\CMTKreg"
perl "C:\CMTKresults\CMTK\bin\munger" -b "C:\CMTKresults\CMTK\bin" -r 02 -f 01 -T 8 -s "template/template16.PIC" "images"
leads to identical results.
Interestingly, I am able to register 8-bit .PIC files to an 8-bit .PIC template without incident. Unfortunately I need to use 16-bit images.
Any suggestions would be greatly appreciated! My apologies if the solution is completely obvious.
Thank you!
Threaded View
Title | Author | Date |
---|---|---|
Gabriella Sterne | May 10, 2016 | |
Gabriella Sterne | Feb 23, 2017 | |
Greg Jefferis | May 10, 2016 | |
Torsten Rohlfing | May 12, 2016 | |