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taznux / lung-image-analysis

A basic framework for pulmonary nodule detection and characterization in CT
https://qradiomics.wordpress.com/portfolio/lung-image-analysis-framwork/
MIT License
32 stars 15 forks source link

What is the proper way to run this? #8

Closed Aneeshers closed 7 years ago

Aneeshers commented 7 years ago

Hi I'm just a Matlab hobbyist, this project seemed very interesting, I'm just wondering what the proper way is to run this project.

Thanks

taznux commented 7 years ago

Hi Aneeshers,

This is a framework for nodule detection and lung image analysis. I have three test code for nodule detection, image convert, and nodule segmentation.

Before you run this, you should have a recent version of MATLAB (after 2013b) because of the table datatype. http://blogs.mathworks.com/loren/2013/09/10/introduction-to-the-new-matlab-data-types-in-r2013b/ And you should have a part or entire LIDC-IDRI database on your disk.

path_data = [pwd '/DATA/LIDC-IRDI']; %dcm files directory

main.m: Simple nodule detection system which has limited accuracy

main_image_to_nrrd.m: DICOM to nrrd converter (main_image_to_nrrd.m) for connection to my another image processing framework (https://github.com/taznux/radiomics-tools). This code has different data path. I'll make a consistent path for next revision.

path_data` = [pwd '/../../LIDC-IDRI/DOI/']; %dcm files directory

main_nodule_segmentation.m: Simple evaluation framework for nodule segmentation.

I'll update README.md with usages soon.

Thanks, Wookjin

Aneeshers commented 7 years ago

@taznux HI thank you so much, I just have another issue/question So when I run the program I inputted a small file with about 133 dicom files, then I get the error

error: matrix cannot be indexed with .
error: called from
    main at line 207 column 1
error: evaluating argument list element number 1
error: called from
    main at line 207 column 1
taznux commented 7 years ago

You cannot run this code on Octave. You have to use MATLAB 2013b or late version.

Aneeshers commented 7 years ago

@taznux Thank you, I will try it on MATLAB, any reason specifically why it won't function on GNU octave?

taznux commented 7 years ago

Even though they have similar syntax, they are different. These links can give you the answers.

https://en.wikibooks.org/wiki/MATLAB_Programming/Differences_between_Octave_and_MATLAB http://stackoverflow.com/questions/12084246/differences-between-octave-and-matlab