mvallieres/radiomics

MATLAB programming tools for radiomics analysis

radiomics's Issues

Install

Is it run directly? I can not run it with matlab 2017b,which just shows a figure without functions. So,any idea?

Incomplete data?

Hi, thanks for posting the data out for everyone to access. I downloaded the .mat files containing the radiomics features. I noticed that the four modalities combined total upto 408 files. Out of these 106 are in T1CE, 107 are in T1W, 108 in T2W, and 87 in T2F. Is there any reason behind the difference in the number of mat files in the four modalities. This also doesn't tally up with the info mentioned [here]. (https://github.com/mvallieres/radiomics/blob/master/STUDIES/LGG_study/TCGA_clinical_INFO.csv)

radiomics features (+ wavelet ?)

Hi. first of all, thank you so much .

i tried to test the code with samples.
I got 44 features.

I'd like to add wavelet based features : e.g. multi-scale textures of variance - five features: LHL, HHL, LLH, LHH, and HHH), entropy (i.e., five features: HLL, LHL, HHL, LLH and HHH), and energy (i.e., two features: HLL and LLH). ...

What i want is all features : 44 * (5+5+2) features.

How can I get all features ?

thank you.

pixelW and related questions

Based on this question (https://stackoverflow.com/questions/59308919/radiomics-package-in-matlab)

I used is this code:

volume = double(rgb2gray(imread('http://www.cs.sjsu.edu/~bruce/images/fall_2016_cs160/lectures/eye_pupil_tracking/grayscale_eye_cropped_to_bounding_box.png')));
mask = ones(size(volume,1),size(volume,2));
[ROIonly,levels] = prepareVolume(volume,mask,'Other',10, 22, 1, 22,'Matrix','Uniform',256);
[GLCM] = getGLCM(ROIonly,levels);
DataGLCM = getGLCMtextures(GLCM)

 
I do not know what is the pixelW so what will be the value? In the case of this png file what shell I use as "Numerical value specifying the in-plane resolution (mm) of 'volume'"? (I used a random number of 10), What shell I used in scale as it is related to pixelW?. When I will use it on eye images I will use the full image like in the case above where mask and volume are the same.
 
Thanks a lot,
Lluis

about the pixelW and slicsS

Hi mvallieres!
I have to process some fundus images and i don't know the number of pixelW and sliceS..... So how to solve this problem?? Thanks!

2D analysis

Hi mvallieres!

Thanks for your codes.

When I use the function "prepareVolume" with a 2D data, I got a error like:

error wavedec3 (line 109)
sizes(level+1,1:3) = size(X);

error waveletBPfilt (line 51)
wDEC=wavedec3(volume,1,wavelet);

error prepareVolume (line 149)
  ROIbox = waveletBPfilt(ROIbox,R,'sym8');

I think that's because the 'size(X)' has 2 , while the 'sizes(level+1,1:3)' has 3. You said the function "prepareVolume" is compatible with 2D analysis. But it looks doesn't work for 2D analysis.

How could I revise it? Thanks!

calcAllFeatureSets_batchLGG :Undefined function or variable 'batchExperiments'.

I run LGG_study masterScript_LGG on OS matlab_R17a run ,as your INSTRUCTIONS,it goes on well ,untill

% A.2 PERFORM FEATURE SET REDUCTION FROM TRAINING SETS
tic, fprintf('\n--> PERFORMING FEATURE SET REDUCTION FROM THE TRAINING SETS WITH %u CORES ... ',nBatch)
calcAllFeatureSets_batchLGG(pathMINE,pathLR,setSize,alpha,delta,nBoot,nBatch,matlabPATH,seeds(1))

Matlab Window:
--> PERFORMING FEATURE SET REDUCTION FROM THE TRAINING SETS WITH 8 CORES ... Undefined function or variable 'batchExperiments'.

Error in calcAllFeatureSets_batchLGG (line 82)
[param] = batchExperiments(setNames,outcomes,nBatch); nBatch = length(param);

Could you please give me a help ?
thanks!!!

LGG_STUDY error

Machine

Ubuntu 16.04

matlab version

R2015b

Error infomation

--> PERFORMING PREDICTION PERFORMANCE ESTIMATION FROM THE TRAINING SETS WITH 8 CORES ... DONE!
时间已过 66.557156 秒。
错误使用 load
无法读取文件 'RESULTS_T1W_T2W_nonIDH1'。没有此类文件或目录。

出错 plotPredictionResults_LGG (line 70)
    results = load(['RESULTS_',fSET,'_',nameOutcome]); results = struct2cell(results); results =
    results{1};

出错 autoChoiceBestModels_LGG (line 66)
    plotPredictionResults_LGG(fullfile(pathExperimentBinary,'RESULTS'),nameOutcomes{o},fSetNames,metric,maxOrder,pathFig)
    
出错 masterScript_LGG (line 190)
autoChoiceBestModels_LGG(pathLR,fSetNames,nameOutcomes,'AUC632',maxOrder,pathFig) % USE THIS LINE
TO REPRODUCE THE RESULTS OF THIS STUDY.

Hi @mvallieres I try to run the masterScript_LGG.m. I have followed the instruction in README in LGG_study folder step by step.But error just happened as above shown.Do you know what is the problem？Thanks.