Lung airway segmentation

cip

(anita khanna) #21

one more thing sir. i am loading and viewing dicom image as ‘dicom_021.dcm’ containing some 450 images. is it possible to convert it to ‘dicom_021/.dcm’ where '’ represents 459 image set using slicer. hope i have put my question correctly


(anita khanna) #22

sorry. Actually i wrote convert to dicom_021/*.dcm’. don’t know why * didn’t show in my earlier message


(Andras Lasso) #23

Actually i wrote

You can go back and edit your posts. Please do so instead of writing additional posts.

* is a formatting character in markdown. If you need verbatim display of text containing formatting characters then select the text and click image button in the editor.


(Andras Lasso) #24

A post was split to a new topic: Show two volumes overlaid


(anita khanna) #25

sir i have attempted lung vessel segmentation. how can i remove very smallbroken pieces of segmented results and also make vessels smooth using slicer?


(anita khanna) #26

how can i view int16 dicom images with HU units in 3D slicer. many codes are with Hu units of dicom images.
sorry to ask but are my questions not relevant to be answered sir.
regards


(Steve Pieper) #27

Slicer should be displaying HU if the dicom header is correct. Do you have a reason to think the pixels are not in HU?


(anita khanna) #28

thanks for reply
sir i want to know two things:

  1. how to give seed points in simple region growing module
  2. after region growing, how can i find areas of segmented region and remove areas smaller than a threshold.
    pl suggest

(Steve Pieper) #29

Hi @anitakh1 - have a look at the segmentation tutorials and documentation - you’ll find lots of ways to do define regions and use thresholds:

https://www.slicer.org/wiki/Documentation/4.8/Training#Segmentation

Cheers,
Steve


(anita khanna) #30

hello. i am stuck badly. i did some segmentation work and stored the image volume as .nrrd using slicer. but when i am opening single images in matlab, image is opening in double format but pixel values as not between [0 1] (as is the case with double image in matlab) but in numbers like 45, 23 etc . this is creating problem for me to run an algorithm in matlab. pl help to read each image in matlab as double image between [0 1].


(Andras Lasso) #31

You can use the nrrd file reader/writer (nrrdread.m and nrrd write.m) in Slicer MatlabBridge, which work correctly: https://github.com/PerkLab/SlicerMatlabBridge/tree/master/MatlabCommander/commandserver

Note that segmentation result is stored in a 4D array, each segment is a 3D array in it.

You may use Slicer’s MatlabBridge extension for running Matlab functions directly from Slicer: https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge

At some point, you may consider moving from Matlab environment to Python, as there are much better and many more tools for medical image computing in Python packages and in Slicer and there are no licensing hassles.


(anita khanna) #32

thanks a lot. sir can i get some training on slicer and matlab bridge module in india. it would be quite helpful


(Andras Lasso) #33

A post was split to a new topic: Vessel tracking algorithm on lung CT


(anita khanna) #34

hello sir. can you please help me. i made some code and applied it on .raw volume data where pixel intensities were positive numbers. but rest of the data i have has HU units both positive and negative. my code is not working properly on these HU units. pl guide me how to get .raw file with all positive pixel values. i am not sure but some window level change is required i think. pl tell me how. my work has stopped because of that. regards


(Andras Lasso) #35

How did you create the .raw file? How did you read it? Did you implement processing in Matlab, Python, or C++?


(anita khanna) #36

I made code in python using simpleitk, numpy etc. but region growing works well when pixel intensity is >0. So how to change pixel range of ,raw n make all positive. Thanks


(anita khanna) #37

Sorry. I think u asked about file. Well i downloaded the file from vessel12 data n did 7zip to get .mhd n .raw folder but HU units are -&+ as usual. I m reading it on slicer.


(Andras Lasso) #38

Have you implemented region growing or you used SimpleITK or VTK filters?


(anita khanna) #39

I used region growing using simpleitk command on raw images with pixel intensity above zero.


(Andras Lasso) #40

Which SimpleITK command?