Hello,
I am trying to use the GLCM Texture Tool (https://imagej.nih.gov/ij/plugins/texture.html) to analyse the degree of organisation in a region of interest. However, as my region of interest has an irregular (non-rectangular) shape, I would need to use an updated version mentioned in the above plugin description.
Could someone advise how to get a version of GLCM Texture Tool working with irregular shapes?
Thank you!
Hi @mariesarazova,
Welcome to the forum.
As far as I know, there isnât an update to that plugin with the feature you want.
Iâd recommend working with the biggest rectangular ROI that fits inside your irregular ROI.
If the rectangle big enough, then the statistics of the smaller area will be close to those of your bigger irregular area.
I see that imagej-ops also has an implementation of texture features similar to what you pointed to. Iâm not so familiar with it, but Iâd expect it can do what you want.
John
Hi,
to come back shortly to the topic, Toby Cornish, who worked on an updated Texture Analyzer, pointed our attention to github (https://github.com/cornish/GLCM-TextureToo) for a newer version v0.008. However, he does not guarantee correctness or functionality of the plugin, as it has long not been worked on.
In my experience, I have had problems making that version run on my ImageJ 1.51u, Java 1.8.0_66 (64bit). However, with the ImageJ 1.51j8, Java 1.8.0_112(64-bit) it works (as in - runs without crashingâŠ).
Also, there is a reference to v0.009, an âin house-modificationâ of v0.008 in Sivchenko et al., 2006 - https://www.tandfonline.com/doi/full/10.1080/23311916.2016.1206679
Hope this helps!
Marie
Hi,
If you are looking for textural analysis, Iâm also working on a ImageJ front end for pyRadiomics software see : pyRadiomics GUI in ImageJ
It will require to install a third party app in python but then you will be able to operate radiomics calculations (including GLCM 2D and 3D) with 200+ radiomics feature with a strong scintific validation (see http://www.radiomics.io)
Salim
Hi Salim
Thank you for making a nice radiomics software.
I downloaded the software (imageJ jar) from URL below.
https://github.com/salimkanoun/pyRadiomics_GUI/releases/download/0.22.1/py_Radiomics.jar
Next, I included âbrain1_image.nrrdâ and âbrain1_label.nrrdâ as a image file and a mask file, respectively (both are sample files of pyradiomics). Then, I pushed âCalculateâ, but nothing happened.
Could you please teach me how to calculate radiomics features?
xackey2001
Yes, you have to put the roi number in the first window
you can select only one roi number (example 1) or a range 1-5
Of course the ROI number you are going to enter have to exist in the mask
Salim
Le mer. 19 juin 2019 Ă 04:26, Motohiko Yamazaki via Image.sc Forum imagej@discoursemail.com a Ă©crit :
Thank you for your kind reply.
I entered the Roi number (=1), and pushed the âCalculateâ buton.
After that, the message âDoneâ is seen.
Where can I see results?
xackey2001
When you clicked on the calculate you should have been asked to define a CSV file location, the program generate the CSV file at the location you have choosen and you will see the results with this file with any spreadsheet reader
Le mer. 19 juin 2019 Ă 09:51, Motohiko Yamazaki via Image.sc Forum imagej@discoursemail.com a Ă©crit :
you should have been asked to define a CSV file location
Unfortunately, such message did not apeared even after I pushed the âCalculateâ.
Is Fiji not supported? Please tell me the supported version of ImageJ.
My OS is windows 7. Should I use windows 10?
xackey2001
It should work but the version you got from the github is old.
Could you try by removing the jar you downloaded and add in Fiji the âNuclear Medicineâ update site, you will download a more recent version of this pyRadiomics plugin.
Le mer. 19 juin 2019 Ă 10:32, Motohiko Yamazaki via Image.sc Forum imagej@discoursemail.com a Ă©crit :
As per your advice, I downloaded a recent version from the âNuclear Medicineâ.
After I clicked âCalculateâ, info window appeared as shown on the uploaded image below.
But I am not asked where to save the CSV file. Am I correct?
xackey2001
Well, I have to fixâŠ
I will try to look at tommorow
I sent an update, the problem was due to a change in the output of pyradiomics in the latest 2.2.0 version.
Please confirm if it is now fixed for you
Best regards,
Salim
The update version successfully worked.
Thank you very much!!
xackey2001
Thank you for your good works.
Iâm also having an issue. Iâm extracting the radiomics feature from DICOM images and itâs a 3D MR image (just a single slice with 3 mm thickness). After inputing Mask & original file, it shows an error.
Here this is:
*E: radiomics.script: Feature extraction failed!
Traceback (most recent call last):
"File ââc:\python\python390\lib\site-packages\radiomics\scripts\segment.pyââ, line 70, in _extractFeatures feature_vector.update(extractor.execute(imageFilepath, maskFilepath, label, label_channel))"
"File ââc:\python\python390\lib\site-packages\radiomics\featureextractor.pyââ, line 272, in execute image, mask = self.loadlmage(imageFilepath, maskFilepath, generallnfo, -_settings)"
"File ââc:\python\python390\lib\site-packages\radiomics\featureextractor.pyââ, line 385, in loadlmage mask = imageoperations.getMask(mask, -kwargs)"
"File ââc:\python\python390\lib\site-packages\radiomics\imageoperations .pyââ, line 51, in getMask raise ValueError(âLabel (%g) not present in mask. Choose from %sâ % (label, labels[labels !:OJ))"
ValueError: Label (1) not present in mask. Choose from (255)
*
Would you give me any idea, what I need to do? I am new in this area.
Thanks
Well i think the solution is in your log
ValueError: Label (1) not present in mask. Choose from (255
You seems to call the results of a label that is not in your mask.
Thanks
Is there any way to change the Label value on ImageJ?
I created binary mask using ImageJ.
in the main view of the PyRadiomics GUI you have a âROI numberâ in which you write your label number.
On you binary mask check the value of your pixel either 0/1 or 0/255 then your mask is 1 or 255
