Success in extracting particles systems

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Shahrokh Nasseri (PhD)

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Nov 18, 2020, 5:23:57 AM11/18/20

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Hello Dear Raul and Dear Pietro

Thank you very much for your guidance.

With your guidance and support, I was able to extract the particles system.

The steps of installation and execution (in Ubuntu 18.04.4 LTS), in order to extract the particles system, are mentioned in the following lines:

Building:

sn@MP:~$ git clone https://github.com/acil-bwh/ChestImagingPlatform.git

...

sn@MP:~$ git checkout 7a4413f

Note: checking out '7a4413f'.

You are in 'detached HEAD' state. You can look around, make experimental

changes and commit them, and you can discard any commits you make in this

state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may

do so (now or later) by using -b with the checkout command again. Example:

git checkout -b <new-branch-name>

HEAD is now at 7a4413f7 ENH: fixing error to load test data

sn@MP:~$ mkdir ChestImagingPlatform-build

sn@MP:~/ChestImagingPlatform$ cd ../ChestImagingPlatform-build/

sn@MP:~/ChestImagingPlatform-build$ /home/sn/cmake-3.10.2-Linux-x86_64/bin/ccmake ../ChestImagingPlatform

...

Page 1 of 1

BUILD_STYLE_UTILS ON

BUILD_TESTING ON

CIP_PYTHON_INSTALL ON

CIP_PYTHON_INSTALL_DIR /home/sn/ChestImagingPlatform-build/CIPPython-install

CIP_PYTHON_INSTALL_DL_TOOLS ON

CIP_PYTHON_SOURCE_DIR /home/sn/ChestImagingPlatform-build/CIPPython

CIP_PYTHON_USE_QT4 OFF

CIP_SUPERBUILD ON

CIP_USE_GIT_PROTOCOL ON

CIP_VTK_RENDERING_BACKEND OpenGL2

CMAKE_BUILD_TYPE Release

CMAKE_INCLUDE_DIRECTORIES_BEFO ON

CMAKE_INSTALL_PREFIX /usr/local

EXTERNAL_PROJECT_BUILD_TYPE Release

FORCE_EXTERNAL_BUILDS OFF

FORCE_SYSTEM_LIBXML OFF

ITK_VERSION_MAJOR 5

PYTHON_EXECUTABLE /home/sn/ChestImagingPlatform-build/CIPPython-install/bin/python2.7

USE_BOOST ON

USE_ITK_4.10 OFF

USE_SYSTEM_Cppcheck OFF

USE_SYSTEM_DCMTK OFF

USE_SYSTEM_ITK OFF

USE_SYSTEM_KWStyle OFF

USE_SYSTEM_SlicerExecutionMode OFF

USE_SYSTEM_Uncrustify OFF

USE_SYSTEM_VTK OFF

USE_SYSTEM_zlib OFF

VTK_VERSION_MAJOR 8

...

Press [c] to configure

...

Press [g] to generate and exit

sn@MP:~/ChestImagingPlatform-build$ make -j 6

...

[ 98%] Linking CXX executable ../../Testing/bin/UpdateParticlesDataTest

[ 98%] Built target UpdateParticlesDataTest

[ 99%] Linking CXX executable ../Testing/bin/GenerateLobeSurfaceModelsTest

[100%] Linking CXX executable ../Testing/bin/FilterConnectedComponentsTest

[100%] Built target GenerateLobeSurfaceModelsTest

[100%] Built target FilterConnectedComponentsTest

[ 94%] No install step for 'CIP'

[ 95%] Completed 'CIP'

[100%] Built target CIP

sn@MP:~/ChestImagingPlatform-build$

Note: As you can see, I changed the value of the ITK_VERSION_MAJOR variable from 4 to 5.

If this is not changed, as mentioned in my message on Nov 16, 2020 at 2:44:18 PM in ChestImagingPlatform-users, I will get error message about itkMultiThreaderBase.h: No such file or directory.

Executing:

sn@MP:~$ export PYTHONPATH=/home/sn/ChestImagingPlatform-build/CIP-build:/home/sn/ChestImagingPlatform-build/CIP-build:/home/sn/ChestImagingPlatform-build/CIPPython-install/lib/python27.zip:/home/sn/ChestImagingPlatform-build/CIPPython-install/lib/python2.7:/home/sn/ChestImagingPlatform-build/CIPPython-install/lib/python2.7/plat-linux2:/home/sn/ChestImagingPlatform-build/CIPPython-install/lib/python2.7/lib-tk:/home/sn/ChestImagingPlatform-build/CIPPython-install/lib/python2.7/lib-old:/home/sn/ChestImagingPlatform-build/CIPPython-install/lib/python2.7/lib-dynload:/home/sn/ChestImagingPlatform-build/CIPPython-install/lib/python2.7/site-packages

sn@MP:~$ export CIP_PATH=/home/sn/ChestImagingPlatform/Scripts

sn@MP:~$ export TEEM_PATH=/home/sn/ChestImagingPlatform-build/teem-build/bin

sn@MP:~$ export ITKTOOLS_PATH=/home/sn/ChestImagingPlatform-build/ITKv4-build/bin

sn@MP:~$ export PATH=$PATH:/home/sn/ChestImagingPlatform-build/CIP-build/bin:/home/sn/ChestImagingPlatform-build/teem-build/bin

sn@MP:~$ cd testCIP/

sn@MP:~/testCIP$ ls

SR_4

sn@MP:~/testCIP$ ConvertDicom --dir SR_4/ -o CT.nrrd

...

DONE.

sn@MP:~/testCIP$ GenerateMedianFilteredImage -i CT.nrrd -o CTFiltered.nrrd

...

DONE.

sn@MP:~/testCIP$ GeneratePartialLungLabelMap --ict CTFiltered.nrrd -o partialLungLabelMap.nrrd

...

DONE.

sn@MP:~/testCIP$ python /home/sn/ChestImagingPlatform/Scripts/cip_compute_vessel_particlesCorrected.py -i CT.nrrd -l partialLungLabelMap.nrrd -r WholeLung --tmpDir /home/sn/testCIP -o particles.vtk --perm -r LeftLung -s 0.625

unu resample -k tent -s x1.220090 x1.220090 x4.254119 -i CT.nrrd -o /home/sn/testCIP/CT_resample.nrrd -c cell

unu resample -k cheap -s x1.220090 x1.220090 x4.254119 -i partialLungLabelMap.nrrd -o /home/sn/testCIP/CT_resamplepartialLungLabelMap.nrrd -c cell

/home/sn/ChestImagingPlatform-build/CIP-build/bin/CropLung --cipr LeftLung -m 0 -v -1000 --ict /home/sn/testCIP/CT_resample.nrrd --ilm /home/sn/testCIP/CT_resamplepartialLungLabelMap.nrrd --oct /home/sn/testCIP/leftLung/CT_leftLung.nrrd --olm /home/sn/testCIP/leftLung/CT_leftLung_partialLungLabelMap.nrrd

Reading CT from file...

Reading label map from file...

Reading label map...

Extracting region and type...

Computing Bounding Box...

0: 299

1: 552

2: 133

3: 474

4: 30

5: 615

0: 299

1: 552

2: 133

3: 474

4: 30

Writing CT cropped image...

Writing cropped label map...

DONE.

/home/sn/ChestImagingPlatform-build/CIP-build/bin/ExtractChestLabelMap -r LeftLung -i /home/sn/testCIP/leftLung/CT_leftLung_partialLungLabelMap.nrrd -o /home/sn/testCIP/leftLung/CT_leftLung_partialLungLabelMap.nrrd

Reading...

Extracting...

Writing...

DONE.

unu 2op gt /home/sn/testCIP/leftLung/CT_leftLung_partialLungLabelMap.nrrd 0.5 -o /home/sn/testCIP/leftLung/CT_leftLung_partialLungLabelMap.nrrd

/home/sn/ChestImagingPlatform-build/CIP-build/bin/ComputeDistanceMap -l /home/sn/testCIP/leftLung/CT_leftLung_partialLungLabelMap.nrrd -d /home/sn/testCIP/leftLung/CT_leftLung_distanceMap.nrrd -s 1 -p -m Maurer

Reading label map...

Skipping downsampling...

Computing distance map...

Writing to file...

DONE.

Distance from wall: 2.0

unu 2op gt /home/sn/testCIP/leftLung/CT_leftLung_distanceMap.nrrd 2.000000 | unu convert -t short -o /home/sn/testCIP/leftLung/CT_leftLung_partialLungLabelMap.nrrd

/home/sn/ChestImagingPlatform-build/CIP-build/bin/ComputeFeatureStrength -i /home/sn/testCIP/leftLung/CT_leftLung.nrrd -m Frangi -f RidgeLine --std 0.700000,4.000000,7 --ssm 1 --alpha 0.63 --beta 0.51 --C 245 -o /home/sn/testCIP/leftLung/CT_leftLung_featureMap.nrrd

Reading CT from file...

0.7 4 7

DONE.

unu 2op x /home/sn/testCIP/leftLung/CT_leftLung_featureMap.nrrd /home/sn/testCIP/leftLung/CT_leftLung_partialLungLabelMap.nrrd -t float | unu heq -b 10000 -a 0.96 -s 5 | unu 2op gt - 0.380000 | unu convert -t short -o /home/sn/testCIP/leftLung/CT_leftLung_mask.nrrd

DONE.

Resetting param groups...

Building param groups...

Starting pass 1...

gageStackBlurGet: no file "/home/sn/testCIP/leftLung/V-000-010.nrrd"; will recompute blurrings

Finished pass 1.

Starting pass 2...

gageStackBlurGet: will reuse 10 /home/sn/testCIP/leftLung/V-%03u-010.nrrd pre-blurrings.

Finished pass 2.

Starting pass 3...

gageStackBlurGet: will reuse 10 /home/sn/testCIP/leftLung/V-%03u-010.nrrd pre-blurrings.

Finished pass 3.

Probing...

gageStackBlurParmScaleSet: !!! This function is deprecated; use gageStackBlurParmSigmaSet instead !!!

Finished probing.

Saving to vtk...

-o particles.vtk_leftLungVesselParticles.vtk -b -i /home/sn/testCIP/leftLung/pass3.nrrd -a NA -i /home/sn/testCIP/leftLung/hevec1.nrrd -a hevec1 -i /home/sn/testCIP/leftLung/hevec0.nrrd -a hevec0 -i /home/sn/testCIP/leftLung/val.nrrd -a val -i /home/sn/testCIP/leftLung/hevec2.nrrd -a hevec2 -i /home/sn/testCIP/leftLung/heval0.nrrd -a h0 -i /home/sn/testCIP/leftLung/heval1.nrrd -a h1 -i /home/sn/testCIP/leftLung/heval2.nrrd -a h2 -i /home/sn/testCIP/leftLung/hess.nrrd -a hess -i /home/sn/testCIP/leftLung/hmode.nrrd -a hmode --irad 0.8 --srad 4 --liveth -90 --seedth -70 --spacing 0.6250496,0.6250496,0.625362069636 --cipr UndefinedRegion --cipt Vessel

Reading file for NA...

Reading file for hevec1...

Reading file for hevec0...

Reading file for val...

Reading file for hevec2...

Reading file for h0...

Reading file for h1...

Reading file for h2...

Reading file for hess...

Reading file for hmode...

Writing poly data...

DONE.

sn@MP:~/testCIP$ ll -h

drwxr-xr-x 4 sn sn 4.0K Nov 16 18:01 ./

drwxr-xr-x 163 sn sn 12K Nov 16 17:35 ../

-rw-r--r-- 1 sn sn 35M Nov 16 13:29 CTFiltered.nrrd

-rw-r--r-- 1 sn sn 38M Nov 16 13:29 CT.nrrd

-rw-r--r-- 1 sn sn 479M Nov 16 17:08 CT_resample.nrrd

-rw-r--r-- 1 sn sn 479M Nov 16 17:08 CT_resamplepartialLungLabelMap.nrrd

drwxr-xr-x 2 sn sn 4.0K Nov 16 18:01 leftLung/

-rw-r--r-- 1 sn sn 733K Nov 16 13:29 partialLungLabelMap.nrrd

-rw-r--r-- 1 sn sn 2.6M Nov 16 18:01 particles.vtk_leftLungVesselParticles.vtk

drwxr-xr-x 2 sn sn 4.0K Nov 11 12:07 SR_4/

sn@MP:~/testCIP$ ll -h leftLung/

drwxr-xr-x 2 sn sn 4.0K Nov 16 18:01 ./

drwxr-xr-x 4 sn sn 4.0K Nov 16 18:01 ../

-rw-r--r-- 1 sn sn 195M Nov 16 17:11 ct-deconv.nrrd

-rw-r--r-- 1 sn sn 107M Nov 16 17:09 CT_leftLung_distanceMap.nrrd

-rw-r--r-- 1 sn sn 281M Nov 16 17:11 CT_leftLung_featureMap.nrrd

-rw-r--r-- 1 sn sn 98M Nov 16 17:11 CT_leftLung_mask.nrrd

-rw-r--r-- 1 sn sn 60M Nov 16 17:08 CT_leftLung.nrrd

-rw-r--r-- 1 sn sn 98M Nov 16 17:09 CT_leftLung_partialLungLabelMap.nrrd

-rw-r--r-- 1 sn sn 793K Nov 16 18:01 hess.nrrd

-rw-r--r-- 1 sn sn 89K Nov 16 18:01 heval0.nrrd

-rw-r--r-- 1 sn sn 89K Nov 16 18:01 heval1.nrrd

-rw-r--r-- 1 sn sn 89K Nov 16 18:01 heval2.nrrd

-rw-r--r-- 1 sn sn 265K Nov 16 18:01 hevec0.nrrd

-rw-r--r-- 1 sn sn 265K Nov 16 18:01 hevec1.nrrd

-rw-r--r-- 1 sn sn 265K Nov 16 18:01 hevec2.nrrd

-rw-r--r-- 1 sn sn 89K Nov 16 18:01 hmode.nrrd

-rw-r--r-- 1 sn sn 2.0M Nov 16 17:51 pass1.nrrd

-rw-r--r-- 1 sn sn 2.0M Nov 16 17:53 pass2.nrrd

-rw-r--r-- 1 sn sn 705K Nov 16 18:01 pass3.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-000-010.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-001-010.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-002-010.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-003-010.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-004-010.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-005-010.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-006-010.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-007-010.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-008-010.nrrd

-rw-r--r-- 1 sn sn 195M Nov 16 17:13 V-009-010.nrrd

-rw-r--r-- 1 sn sn 89K Nov 16 18:01 val.nrrd

sn@MP:~/testCIP$

I must mentioned that I edited cip_compute_vessel_particles.py with to add the paths to executable files CropLung, ExtractChestLabelMap, ComputeDistanceMap and ComputeFeatureStrength and renamed it to cip_compute_vessel_particlesCorrected.py.

The result is shown in the following figure.

Best regards.

Shahrokh

Shahrokh Nasseri

Assistant Professor of Medical Physics

Department and Research Center of Medical Physics

Mashhad University of Medical Sciences

Mashhad, Iran

Tel: +98 513 8002328
Fax: +98 513 8002 320
e-mail: nase...@mums.ac.ir

San Jose Estepar, Raul,Ph.D.

unread,

Nov 18, 2020, 7:56:34 AM11/18/20

to Shahrokh Nasseri (PhD), chestimagingp...@googlegroups.com

Hi Shahrokh,

I’m glad to hear that you were able to execute the pipeline.

Thank you for sharing your steps with the list.

Raul

On Nov 18, 2020, at 5:25 AM, Shahrokh Nasseri (PhD) <Nase...@mums.ac.ir> wrote:

External Email - Use Caution

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Best regards.

Shahrokh

Shahrokh Nasseri

Assistant Professor of Medical Physics

Department and Research Center of Medical Physics

Mashhad University of Medical Sciences

Mashhad, Iran

Tel: +98 513 8002328
Fax: +98 513 8002 320
e-mail: nase...@mums.ac.ir

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