main_script.py

Running /home/bic/Desktop/newoutput/PythonScripts/skull_strip.py
/usr/bin/python3 /home/bic/Desktop/newoutput/PythonScripts/skull_strip.py
Skull stripping ...
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/02input/T1.nrrd -mask /home/bic/Desktop/02input/brainmask.nrrd -outfile /home/bic/Desktop/newoutput/SkullStripping/T1_stripped.nrrd
exit with success

exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/02input/new.mha -outfile /home/bic/Desktop/newoutput/FinalMasking/T1_MID00.nrrd -mask /home/bic/Desktop/02input/brainmask.nrrd
Cutting below AC-PC line
Creating coronal mask
Coronal mask created
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/T1_MID00.nrrd -outfile /home/bic/Desktop/newoutput/FinalMasking/new_MID01.nrrd -mask /home/bic/Desktop/newoutput/FinalMasking/coronal_mask_70.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/new_MID01.nrrd -outfile /home/bic/Desktop/newoutput/FinalMasking/new_MID02.nrrd -extractLabel 3
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/new_MID02.nrrd -outfile /home/bic/Desktop/newoutput/FinalMasking/new_MID03.nrrd -conComp 1
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/02input/brainmask.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion00.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion00.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -threshold 0,0 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01_inv.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/new_MID03.nrrd -mask /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01_inv.nrrd -outfile /home/bic/Desktop/newoutput/FinalMasking/new_Partial_CSF.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/new_Partial_CSF.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_Ero.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_Ero.nrrd -mask /home/bic/Desktop/newoutput/FinalMasking/brainmask_Erosion.nrrd -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_Masking.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_Masking.nrrd -conComp 1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp.nrrd

/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -threshold 0,0 -outfile /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageMath /home/bic/Desktop/newoutput/FinalMasking/new_Partial_CSF.nrrd -mask /home/bic/Desktop/newoutput/FinalMasking/newPartial_conComp_dil.nrrd -outfile /home/bic/Desktop/newoutput/new_FINAL_QCistern.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.5-Linux(2)/Auto_EACSF-1.7.5-Linux/bin/ImageStat /home/bic/Desktop/newoutput/new_FINAL_QCistern.nrrd -label /home/bic/Desktop/newoutput/new_FINAL_QCistern.nrrd -volumeSummary
Auto_EACSF finished

Auto_EACSF pipeline exited with code 0