Craniosynostosis Code Comments

DataDriver:\\10.54.13.33\Linguraru-Lab\Linguraru Lab 1 I rebuilt the codes from Carlos for the project "Craniosynostosis" under so far newest Ubuntu Linux 14.04 and Slicer4. It took me a lot of time due to the compilation problems. The results may be different from the Carlos's results due to the following change 1. All files using "BRAINSFit" module have the following change (note: symbol '......' indicates some parts ignored) Carlos: std,err = subprocess.Popen(["/home/cmendoza/CNMCModules/BRAINSStandAlone-build/lib/BRAINSFit",......,'--useSimilarity3D',......],                 stdout=subprocess.PIPE,stderr=subprocess.PIPE).communicate() ours: std,err = subprocess.Popen(["/home/jinqi/Slicer4-SuperBuild-Debug/Slicer-build/lib/Slicer-4.3/cli-modules/BRAINSFit",.......,'--useScaleSkewVersor3D',.....],                 stdout=subprocess.PIPE,stderr=subprocess.PIPE).communicate() The following changes will not affect the experimental results and they are for compilation problems 1. in GCoptimization.h file, add the following line at the beginning: #include <cstddef> 2. in Energy.h file, change like this what_segment add_tweight add_edge becomes this->what_segment this->add_tweight this->add_edge 3. compile problem with original module "BRAINSResample" in directory "BRAINSStandAlone"; the module is already in Slicer, We use the built in module in Slicer. 4. "wrapper" , "Hausdorff" is not in slicer, we have to manually build and add 5. modelmaker python example http://www.na-mic.org/Wiki/index.php/AHM2012-Slicer-Python 6. to compile "Hausdorff" module, makefile.txt 7. slicer module compiling: mkdir MyModule-build     cd MyModule-build     cmake -DSlicer_DIR:PATH=/path/to/Slicer-Superbuild/Slicer-build ../MyModule $     make Program generated file "Batch/RegistrationFailedNovember.csv": include all cases for test. Compile "TemplateBuilder" module: fatal error: boost/algorithm/string.hpp: No such file or directory|, solution:http://stackoverflow.com/questions/12241152/boost-no-such-file-or-directory Compile "CurvatureCompute" module:  need to compile and install "boost" package and compile and install VTKv6  in slicer with the instruction in https://github.com/daviddoria/PointSetProcessing and http://www.vtk.org/Wiki/VTK/Building/Linux, using ccmake to ensure set Module_vtkInfovisBoost=ON and Module_vtkInfovisBoostGraphAlgorithms=ON, and you probably should set up some options using ccmake if you have the following error notices: /usr/bin/ld: cannot find -lvtkWrappingPythonCore /usr/bin/ld: cannot find -lvtkViewsQt /usr/bin/ld: cannot find -lvtkGUISupportQt /usr/bin/ld: cannot find -lvtkRenderingQt /usr/bin/ld: cannot find -lvtkGUISupportQtOpenGL /usr/bin/ld: cannot find -lvtkGUISupportQtSQL /usr/bin/ld: cannot find -lvtkRenderingFreeTypeFontConfig /usr/bin/ld: cannot find -lvtkFiltersPython /usr/bin/ld: cannot find -lvtkGUISupportQtWebkit   8. Matlab source codes for face recognition via sparse coding: http://www.mathworks.com/matlabcentral/fileexchange/30893-robust-face-recognition-via-sparse-representation-implementation 9. slicer build label map: http://www.slicer.org/slicerWiki/images/6/69/InteractiveEditorTutorial_Slicer3.6-SoniaPujol.pdf 10. bash scripts for building cranio modules: #!/bin/bash BuildModule(){ Src_Dir=$1 echo $Src_Dir Build_Dir="$Src_Dir""-build" rm -rf $Build_Dir mkdir $Build_Dir cd $Build_Dir cmake -DSlicer_DIR:PATH=/home/jqi/MyProjects/Slicer-SuperBuild-Debug/Slicer-build $Src_Dir make } BuildModule $1 11. qmake version choose: https://harishnavnit.wordpress.com/2014/03/24/handling-multiple-versions-of-qt/ Qt4.7.4 install: http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Developers/Build_Instructions/Prerequisites/Qt#Linux qmake directory: /home/jqi/QtSDK/Desktop/Qt/474/gcc/bin 12. nice surgical planning paper: http://mirc.uzleuven.be/MedicalImageComputing/publications.php?advancedSearch=1&author=T.+Clijmans&minYear=1972&lang=nl&printFriendly=1 a) Frontoorbital advancement in coronal suture craniosynostosis: a quantitative preoperative assessment 95326-246161-1-PB 13. surface segmentation: http://www.ipb.uni-bonn.de/projects/fastfps/