tomdoel / pulmonarytoolkit Goto Github PK

Hello，I don‘t know How to save segmentation results in NIFTI format？
I use the “export segmentation ” at GUI ，then I get an RGB image in DICOM format.
I was wondering where I should find the original segmentation results in MATLAB.

Thanks for the nice toolkit. Is there documentation to get started on using PTK in batch mode? I would like to run airway segmentation on a bunch of CT scans without going through the GUI.

When launching PTK for the first time, if the GitHub RSA key fingerprint has not been added to the authorized_hosts then the update check may wait silently for input. The (unreported) message is "The authenticity of host [...] can't be established. RSA key fingerprint is [...]. Are you sure you want to continue connecting (yes/no)? and yes or no should be entered to proceed.
The problem is caused because git remote update cannot be run in a way that avoids this message, Matlab's system command swallows the output by default.

If updating to PTK 0.6 causes problems, please close all figures and then clear Malab's class definitions as follows:

close all
clear all classes

First of all, thank you for providing the software. I made the following error when I clicked the coronal analysis button while running: The plugin PTKSaveCoronalAnalysisResults failed with the following error: The unidentified field name is called "SetPreferredOrientation".; Exception message: The unidentified field name is "SetPreferredOrientation".: PTKDivideLungsIntoCoronalBins.RunPlugin(can you help me,thanks) @tomdoel.

Thank you for your great work!I can not load the .nii file when I used the software.

When using the capture tool to create a screenshot, the vertical capture is misaligned if using macOS full screen mode

Sorry for another question. After manage to load CT images, click any module, it always failed and gave some the following information:

The plugin PTKSpongeModel failed with the following error: Undefined function 'ordf' for input arguments of type 'double'

Could you help me to resolve the problem? I am using matlab 2015a on Window 7.

Thanks

Hello!!

I can't load nii files here. For lobe Segmentation!! How to do that??

Hello, I need to change the coordinate system from PTK coordinates to DICOM coordinates (based on tutorial 2), but i can't do it. Is anyone able to help me? Thanks thanks,
Monica

First of all, thank you for your amazing work, Good Job !
As I tested for a long time, this program is not able to seperate some lung lobes if fissureness is thin or irregular , 'correctly' ; there are colour overflows in segment > lobes section.
How can I improve this, in which '.m or .c' file(s) part , I need to upgrade ?

Hello.

This software really looks great. However, when we try to run a variety of different functions including segmentation of the lungs, lobes, and segments, I am receiving the following error:

The plugin PTKLeftAndRightLungs failed with the following error: Underfined function ‘PTKWatershedFromStartingPoints’ for input arguments type ‘int16’;

The airway segmentation works fine.

Thanks

Hello, Tom
Thanks so much for your nice code, it's very clear. I spent a week analyzing it,but sometimes I didn't know why u dealt it in that way(I can understand your code, but I don't know why..).

Could u give me a list of paper that you refer to ?
I'll keep focusing on your work.

Hello,
thanks for developing Pulmonary Toolkit.
Maybe, I just did something wrong while importing the data, but every single slice from the measurement imported as an individual patient. So the result is about 200 imported patients in patient browser. Is there any possibility how to delete multiple patients in one operation? Or an option to reset all settings of PTK?
Thank you in advance.

Hi,
When I try to use the function, PTKSaveAs, to save the data, it always shows that Undefined function or variable 'PTKSaveAs'. Even when I try to do doc PTKSaveAs, it always shows that No results for PTKSaveAs. Is there any way to save the data into mhd file or nii file without using GUI.

The links pointing to older googlecode distribution are not accessible. For example,
https://pulmonarytoolkit.googlecode.com/svn/trunk/Documentation/PTK%20-%20Tutorial%204.pdf

The UI will round the window and level values entered in the text boxes to the nearest integer.
For most Dicom images this is the preferred behaviour; however when dealing with images of floating point values it might be desirable to set a non-integrer value.

May require changes to:

• MimPluginLabelEditBox
• MimPluginLabelSlider
• MimViewerPanelToolbar
• MimViewerPanelCallback:ModifyWindowLevelLimits
  and consideration of how the window/level values affect other parts of the codebase

asking passward

when i write ' file_infos = PTKDicomUtilities.GetListOfDicomFiles(source_path);', it says 'Undefined variable "PTKDicomUtilities" or class PTKDicomUtilities.GetListOfDicomFiles". i defined file path in source_path. please help

How could I change the coordinate system from PTK coordinates to DICOM coordinates (based on your tutorial 2? Could I change it from the GUI?

I used PTK to load up a scan recently. Its compressed Dicom images of ARDS patient.
It loads fine on ITK-snap and 3D slicer.
But PTK zooms it when imported and seems to crop out the image. Is there any setting i should change. Thanks.

I have problems in importing nifti images into PTK. It showed error: "Failed to load dataset due to error: Cell contents reference from a non-cell array object".

Hi, I was trying to change the name of the output .csv to the accession number of the dicom image?

The plugin PTKLobes failed with the following error: Undefined function or variable 'PTKLobeMapForMRI'.
The plugin PTKLobes failed with the following error: Undefined function or variable 'PTKLobeMapForMRI'.
The plugin PTKSaveLobarAnalysisResults failed with the following error: Undefined variable "obj" or class "obj.Reporting.Error".
The plugin PTKSaveLungAnalysisResults failed with the following error: Undefined variable "obj" or class "obj.Reporting.Error".
The plugin PTKSaveADCAnalysisResults failed with the following error: Undefined variable "obj" or class "obj.Reporting.Error".
The plugin PTKSaveCoronalAnalysisResults failed with the following error: Undefined variable "obj" or class "obj.Reporting.Error".
The plugin PTKSaveLungAnalysisResults failed with the following error: Undefined variable "obj" or class "obj.Reporting.Error".
The plugin PTKAirwayDistanceTransform failed with the following error: Undefined variable "obj" or class "obj.Reporting.Error".
The plugin PTKCarina failed with the following error: Undefined variable "obj" or class "obj.Reporting.Error".
The plugin PTKAirwayDistanceTransform failed with the following error: Undefined variable "obj" or class "obj.Reporting.Error".

How can I solve this issue? In every class I have this same problem Undefined variable "obj" or class "obj.Reporting.Error"

Hi,
This project seems well advanced!
Would you have stories to share regarding the use of PTK (success in discovery, use-case, ...)?
Thanks :)

It seems the 'win-gui' part is missing from the prebuilt release 1.0.0?

hello tomdoel,

your code looks nice and the lung segmentations using the GUI works well.
But if I try to do some automatic segmentation, using your tutorial "TK - Tutorial 3.pdf" something is going wrong....

If I try:

file_infos = PTKDiskUtilities.GetListOfDicomFiles(source_path);

this error occures:

The class PTKDiskUtilities has no Constant property or Static
method named 'GetListOfDicomFiles'.

The source_path includes mhd and raw files.
do you have any advice? would be great!

Thanks

split() was introduced in R2016b and therefore this command fails in previous versions.
This is only used in the Windows update codepath

I would like to edit the airway segments and recalculate radius and center-line for the edited airways. Current options support adding/erasing predetermined patches based on intensity threshold. Is it possible to add regions to airway segments using a freehand polygon drawing tool? As an alternative, is it possible to calculate radius and center-line for manual segmentation?

Dear Developers，
When I use the "lung" tool, I encounter the following error，
Error in PTKWatershedFromStartingPoints(PTK1.0.1) : PTKWatershedMeyerFromStartingPoints has not been compiled. You must compile using mex PTKWatershedFromStartingPoints. Alternatively, use the slower Matlab equivalent function mex PTKWatershedFromStartingPointsMatlab().
Stack:PTKWatershedFromStartingPoints(12); SeparateLungs(186); PTKSeparateAndLabelLungs(30); PTKGetLeftAndRightLungs(16); PTKLeftAndRightLungsInitialiser.RunPlugin(55); MimContextHierarchy.GetResultRecursive(192); MimDatasetResults.GetResult(126); MimDatasetCallback.GetResult(87); PTKLeftAndRightLungs.RunPlugin(50); MimContextHierarchy.GetResultRecursive(192); MimDatasetResults.GetResult(126); MimDataset.GetResultWithCacheInfo(148); MimGuiDataset.RunPluginTryCatchBlock(683); MimGuiDataset.RunPlugin(449); MimGuiBase.RunPluginCallback(604); PTKSegmentLungs.RunGuiPlugin(33); MimGuiBase.RunGuiPluginCallback(581); MimGuiPluginWrapper.RunPlugin(21); @(varargin)tool_wrapper.RunPlugin(varargin{:})(255); MimPluginLabelButton.ButtonClickedCallback(48); @(varargin)obj.ButtonClickedCallback(varargin{:})(40); GemButton.ButtonClickedCallback(134); @(varargin)obj.ButtonClickedCallback(varargin{:})(109); \n

I look forward to your help, thank you very much!
Guo Weiqi

Install Instruction and Tutorial 404 not found

Some full-body CT datasets may not process correctly due to a problem with finding the region of interest (ROI) for full-body CT datasets.

As a workaround you can export the lung region using a suitable viewer such as OsiriX. For best analysis results make sure the exported region includes the whole of the lung.

This is due to the way Matlab overrides mouse callbacks when using pan/zoom tools.
Workaround: Select a different tool (e.g. 'w' for window/level) before changing series/patient.

This issue will be fixed in a future release.

Hello Mr. Tom Doel
I am Amir Zamanpour, I am medical imaging student at Mashhad university of medical science. first of all, thanks for your useful app(Pulmonary Toolkit), I want to use it for processing lung CT images, I succeed to use GUI pulmonary toolkit in MATLAB and save CSV file by Lung Analysis, but I need to use script code about that, I read "PTK - Tutorial 3" pdf file and write and run script file for load and auto segment lung right now but I need to extract lung promoters(like CSV file) in workspaces in MATLAB but I do not know which function to use? (can you help me about that).

May I ask if there are samples of lung imaging analysis in the file that I cannot find, or if there are any channels to obtain them @kbur030 @tomdoel @kbur030 @sevketasurgan

I am getting the following error while segmenting lung field or lobel using the toolkit
The plugin PTKlobes failed with the following error:
Subscript indices must either be real positive integers or logicals.

Thanks for developing this fantastic tool. When I load lung Dicom data, it popped up a message box saying 'No appropriate method, property or field 'GetKey for class PTKPluginResultsInfo'.

could you help me resolve this issue?

In addition, could you put some test data for the user to test?

PTKAddPaths;
ptk_main = PTKMain;
Error: File: PTKMain.m Line: 62 Column: 5
Function definitions in a script must appear at the end of the file.
Move all statements after the "PTKMain" function definition to before the first local function
definition.

Can occur if the underlying pixel data values are negative (or more generally have an intercept of -1024). This is due to PTKLungInteriorNonParenchymaPoints not converting the minimum value correctly.

Hi, tomdeol.
Thanks for your great work!
When I use the "Segment the segments" in toolkit. Two errors when I deal with different dicom sequences.

1. The plugin PTKPulmonarySegments failed with the following error: Error in function SeparateSmallestBranchByRadius: Could not subdivide the tree into exactly the desired number of branches.
2. The plugin PTKPulmonarySegments failed with the following error: Attempt to access sample_image(16,18,29)；As size(sample_image)=[2,2,2], is out of range。
   Thanks
   Gu Yu.