Note: file names have to be matched exactly
script_to_Cuneyt
Notes for Penn PICSL Pipeline for Cuneyt Yilmaz and Connie Hsia’s Canine Data
PICSL Pipeline
Given the insp/exp lung CT files (in NIFTY format, .nii.gz) and the corresponding lung masks files, compute the deformation between inspiration and expiration through image registration. Stains are further computed from the resulting deformation fields. A .csv file is generated by collecting the statistics from different files.
- Binary programs Some binary programs have precompiled binary versions. Others need to be compiled with ITKv4 from scratch.
1.1 ANTS http://www.picsl.upenn.edu/ANTS/ binary available or compile from scratch
1.2 c3d http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Documentation binary available
1.3 Nick’s Utilities https://github.com/ntustison/Utilities Need ITKv4 to compile
- Scripts Scripts of bash and perl are saved in
https://github.com/songgang/script_to_Cuneyt under the folder cuneyt
- Execute Scripts (bash + perl)
3.0 Generate whole lung masks from Cuneyt's provided lobe masks, simply merging them into one file batch_lung_convert_mask_Mar2013.sh
3.1 Batch registration + compute strain: batch_cuneyt_jan2012_lung_registration_tmp.sh
It will iterate over a list of subjects. The subject list should be easily idetified in the begining of the script. For each subject, it will call cuneyt_jan2012_lung_registration_with_mask_tmp.sh
(This needs bash. You can run it on grid using qsub, or just one by one by changing the line containing "qsub" to its equivalent part like using "bash".)
3.2 After the batch is completed, call the follow script to collect all the numbers into .csv files. read_results_Mar2013.pl (This needs perl.)
3.3 Convert deformation files to VTK (TODO: needs confirm) batch_lung_convert_deformation_field_to_vtk.sh
It will iterate over a list of subjects. For each subject, it will call convert_deformation_field_to_vtk.sh