Find for help for extraction radiomics features with nii image

[李卓然]

Dear groups:

     I used your great toolkit pyradomics to exam in a example in following:

from radiomics import featureextractor,getTestCase

import six

import sys, os

dataDir = '/usr/kzhao/MCAD/useful_tool/pyradiomics-master'

imageName, maskName = getTestCase('brain1', dataDir)

print(imageName)

print(maskName)

params = os.path.join(dataDir, "examples", "exampleSettings", "Params.yaml")

print(params)

extractor = featureextractor.RadiomicsFeaturesExtractor(params)

# print(extractor)

result = extractor.execute(imageName, maskName)

but my data is nii mri data, I test for much times ,but no a right results. So can you help me, how to change your toolkit in python scirpt. 

          Thank you and very best.

         Yours 

                                                                           Kunzhao-Brainnetome

[Joost van Griethuysen]

Dear Kunzhao,

what do you mean with 'not right'? Could you attach a logfile generated using level DEBUG. It usually contains a lot of information pointing out what's going wrong.

Regards,

Joost

Op zaterdag 26 mei 2018 12:13:22 UTC+2 schreef 李卓然:

[Carlos Martín]

I am experimenting weird results also. I have nifti files for MR and segmentation of 3 regions. I am not able to generalize the model with weird results. My question is, if I have 3 segmentations, should I receive in the extraction all the features for each of the three regions? For example,
3 times this:
        "original_shape_Flatness": 0.4068389581378348,
        "original_shape_Sphericity": 0.6573231032731822,
        "original_shape_Elongation": 0.8070320951604483,
        "original_shape_Maximum3DDiameter": 102.09750444385826,
        "original_shape_LeastAxis": 40.01589566100229,
        "original_shape_SurfaceArea": 23930.336831353965,
        "original_shape_MajorAxis": 98.35807230497608,
        "original_shape_SurfaceVolumeRatio": 0.1289981362079858,
        "original_shape_Maximum2DDiameterRow": 101.88531703243191,
        "original_shape_MinorAxis": 79.37812116822771,
        "original_shape_Maximum2DDiameterSlice": 96.06168601222083,
        "original_shape_Maximum2DDiameterColumn": 84.52082171308713,

[Kim O]

Hi Carlos, 

How did you get any output with .nii files? 
I have .nii.gz and can't seem to make it work. Thanks!

[Andrey Fedorov]

Sorry for the delayed replies!

Carlos: if you have multiple labels in your segmentation file, my understanding is that you will need to run extractor for each individual label. By default, the label value that will be used is 1. This is if I traced the code correctly. I am sorry, it is indeed not obvious from the documentation. We should clarify this.

Kim O: .nii.gz should work just fine. If it doesn't work, most likely the cause of the problem is in something else. Please provide the error log so we can understand what is going on.