hsokooti
DIR-lab 4DCT dataset
I'm trying to load the DIR-lab 4DCT dataset, but I've run into some trouble.
I downloaded the dataset from dir-lab.com, and applied the following pre-processing steps:
-downloaded all 10 data sets. -renamed *-ssm.img to *_s.img (to silence errors from dirlab.py). -ran the dirlab.py module on the img files. -copied the resulting mha directory to /srv/mymachine/hsokooti/Data/DIR-Lab/4DCT/.
However, running RegNet3D.py throws the following error:
[MainThread ] ---------------------------------Fri Nov 9 11:21:44 2018--------------------------------
[MainThread ] ----------------------------------start experiment------------------------------
[MainThread ] number of images in the last chunk=12
[MainThread ] SyntheticDeformation[generation]: start DIR-Lab_4D/3D_max7_D9//T40/case2/Dsmooth0/DNext3/nextIm.mha
[MainThread ] Process Process-1:
[MainThread ] Traceback (most recent call last):
[MainThread ] File "/usr/lib/python3.5/multiprocessing/process.py", line 249, in _bootstrap
[MainThread ] self.run()
[MainThread ] File "/usr/lib/python3.5/multiprocessing/process.py", line 93, in run
[MainThread ] self._target(*self._args, **self._kwargs)
[MainThread ] File "/home/markemus/dev/RegNet/functions/reading/direct_1st_epoch.py", line 49, in run
[MainThread ] self.fill()
[MainThread ] File "/home/markemus/dev/RegNet/functions/reading/direct_1st_epoch.py", line 85, in fill
[MainThread ] mode_synthetic_dvf='generation'
[MainThread ] File "/home/markemus/dev/RegNet/functions/synthetic_deformation.py", line 63, in get_dvf_and_deformed_images
[MainThread ] generate_next_im(setting, im_info=im_info)
[MainThread ] File "/home/markemus/dev/RegNet/functions/synthetic_deformation.py", line 495, in generate_next_im
[MainThread ] original_im_sitk = sitk.ReadImage(su.address_generator(setting, 'originalIm', **im_info_su))
[MainThread ] File "/home/markemus/.local/lib/python3.5/site-packages/SimpleITK/SimpleITK.py", line 8614, in ReadImage
[MainThread ] return _SimpleITK.ReadImage(*args)
[MainThread ] RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:89:
[MainThread ] sitk::ERROR: The file "/srv/markemus-VirtualBox/hsokooti/Data/DIR-Lab/4DCT/mha/case2/case2_T40_RS1.mha" does not exist.
[MainThread ] total number of variables 1116164
[Thread-4 ] SyntheticDeformation[reading]: waiting 5s for DIR-Lab_4D/3D_max7_D9//T40/case2/Dsmooth0/DNext3/nextIm.mha
Is there an additional/different preprocessing step I need to do? Renaming */case2_T40.mha to */case2_T40_RS1.mha seems to fix this error and creates a nextIm.mha file, but there are more errors after that.
The script functions.preprocessing.dirlab.py is just a conversion from binary files to mha extension. In order to make the voxel spacing isotropic, you can run the script functions.preprocessing.resampling_isotropic.py. The image case2_T40.mha has the voxel spacing of [1.16, 1.16, 2.5] mm, but after resampling the voxel size of case2_T40_RS1 is [1, 1, 1] mm. RS1 stands for resampling to 1 mm.
Thank you, much appreciated.
New error:
Traceback (most recent call last):
File "/home/markemus/dev/RegNet/functions/preprocessing/resampling_isotropic.py", line 34, in <module>
resampling(data='DIR-Lab_4D', spacing=[1, 1, 1], requested_im_list=['Im', 'Mask', 'Torso'])
File "/home/markemus/dev/RegNet/functions/preprocessing/resampling_isotropic.py", line 25, in resampling
im_raw_sitk = sitk.ReadImage(su.address_generator(setting, 'original'+requested_im+'Raw', **im_info_su))
File "/home/markemus/.local/lib/python3.5/site-packages/SimpleITK/SimpleITK.py", line 8614, in ReadImage
return _SimpleITK.ReadImage(*args)
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:89:
sitk::ERROR: The file "/srv/markemus-VirtualBox/hsokooti/Data/DIR-Lab/4DCT/mha/case1/Lung_Filled/case1_T00_Lung_Filled.mha" does not exist.
I figured chest_segmentation.py was my next step, so I ran that and got:
/usr/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/usr/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
sh: 1: E:/PHD/Software/Works_Other/LungSegmentation/ptpulmo.exe: not found
Aside from the path, it looks like there's a missing dependency ptpulmo.exe. I couldn't find it online, is that proprietary?
Thank you for pointing out to this issue. The package ptpulmo is a commercial software. However, several free packages for lung segmentation are available. For instance, lung-segmentation-3d. You can also take a look at the LOLA11 challenge.
The accuracy of torso or lung segmentation is not that important for the RegNet.
Our data is formatted very differently so we're going to rebuild the graph on our own in the end, but thank you for all your help.