GenParaMeshCLP

Marco P — Wed, 09 Jul 2014 15:32:27 GMT

Dear Rodent Cortical Thickness Analysis experts,

I'm using Rodent Thickness to estimate the cortical thickness. Installation and first steps work fine but at some point an error occurred with GenParaMeshCLP and I'm not able to solve it by myself. Could you kindly offer me some support and help me to diagnose the error? I report here the error so you can have an idea of what happened. thanks in advance for your precious support.
Marco

| Searching the softwares...DONE
| Searching the softwares...DONE
| Searching the softwares...DONE
| Generating Dataset csv file...DONE
| Generating Dataset csv file...DONE
| Creating output directory...
| $ mkdir /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing
| Creating Script directory...
| $ mkdir /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Script
| Creating output directory...
| $ mkdir /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing
| Creating Script directory...
| $ mkdir /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Script
| Generating config file...DONE
| Generating Dataset csv file...DONE
Status: Start /home/imaging/tools/RodentThickness_package_v1.1/Application/measureThicknessFilter --mr --sbt --workdir /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM --ids 10 --idl 5 --idh 0 --ttrns 100 /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/prova.nrrd /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1_measurementoutput.nrrd
run: '/home/imaging/tools/RodentThickness_package_v1.1/Application/measureThicknessFilter' '--mr' '--sbt' '--workdir' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM' '--ids' '10' '--idl' '5' '--idh' '0' '--ttrns' '100' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/prova.nrrd' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1_measurementoutput.nrrd'
Status: Finish: Execution time 332217ms
Status: Start /home/imaging/tools/antsbin/bin/ImageMath /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/prova.nrrd -extractLabel 10 -outfile /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentation.nrrd
run: '/home/imaging/tools/antsbin/bin/ImageMath' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/prova.nrrd' '-extractLabel' '10' '-outfile' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentation.nrrd'
Status: Finish: Execution time 300ms
Status: Start /home/imaging/tools/RodentThickness_package_v1.1/Application/SegPostProcessCLP /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentation.nrrd /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentationSegPostProcess.nrrd --UseUnitSpacing
run: '/home/imaging/tools/RodentThickness_package_v1.1/Application/SegPostProcessCLP' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentation.nrrd' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentationSegPostProcess.nrrd' '--UseUnitSpacing'
Status: Finish: Execution time 300ms
Status: Start /home/imaging/tools/RodentThickness_package_v1.1/Application/GenParaMeshCLP --EulerFile --outEulerName /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/EulerFile/Euler_1.txt /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentationSegPostProcess.nrrd --label 1 /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1_para.vtk /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1_surf.vtk
run: '/home/imaging/tools/RodentThickness_package_v1.1/Application/GenParaMeshCLP' '--EulerFile' '--outEulerName' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/EulerFile/Euler_1.txt' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentationSegPostProcess.nrrd' '--label' '1' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1_para.vtk' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1_surf.vtk'
Error: /home/imaging/tools/RodentThickness_package_v1.1/Application/GenParaMeshCLP terminated with an exception: Child aborted
Status: Finish: Execution time 300ms
Error: terminate called after throwing an instance of 'itk::ImageFileReaderException'
Error: what(): /NIRAL/work/mjacquem/CorticalSlicer/ITKv4-install/include/ITK-4.4/itkImageFileReader.hxx:143:
Error: Could not create IO object for file /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentationSegPostProcess.nrrd
Error: The file doesn't exist.
Error: Filename = /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentationSegPostProcess.nrrd
Status: Start /usr/bin/python /home/imaging/tools/RodentThickness_package_v1.1/batchmakeScript/../pythonscript/VerifyEulerScript.py /media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/EulerFile/Euler_1.txt
run: '/usr/bin/python' '/home/imaging/tools/RodentThickness_package_v1.1/batchmakeScript/../pythonscript/VerifyEulerScript.py' '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/EulerFile/Euler_1.txt'
Status: Finish: Execution time 300ms
Error: Traceback (most recent call last):
Error: File "/home/imaging/tools/RodentThickness_package_v1.1/batchmakeScript/../pythonscript/VerifyEulerScript.py", line 13, in
Error: fin = open(inputtxt)
Error: IOError: [Errno 2] No such file or directory: '/media/DATA1/experiments/ex-vivo/anatomical_networks/BIG_anatomical_networks/Rodent_Thickness/test2/Processing/1.MeasurementandSPHARM/EulerFile/Euler_1.txt'
Euler number is different of two
| Running Failed...

Question about parcellation

Michael Craig — Tue, 08 Apr 2014 18:11:05 GMT

Hello,

Is it possible to use this package to parcelate the cortex into distinct regions, then find the volume for each region?

thanks,
Mike

Welcome to Help

Marie Jacquemard — Tue, 26 Feb 2013 19:35:01 GMT

Welcome to Help

NITRC Rodent Cortical Thickness Analysis Forum: help

GenParaMeshCLP

Question about parcellation

Welcome to Help