problem related to use module

[1191620]

How can I install it?

[Mehrancd]

you can download the module and add it to 3D Slicer-->Edit-->Application Settings-->Modules, then add the path of the module to "Additional module paths" and restart. It will appear somewhere in module lists in Example.
The module needs tensorflow, scikit,.... that automatically installs them. if you receive an error, push apply again might solve it.
if you need a fast processing, you should increase the voxel size using "resample scaler volume" tool.

Let me know if you have problem to install it

[1191620]

Thanks a lot for your help.Could you explain how download the module?? 😁Sent from my Samsung Galaxy smartphone. -------- Original message --------From: Mehran Azimbagirad ***@***.***> Date: 15/06/2022 19:21 (GMT+03:30) To: Mehrancd/TsallisBrainSegmentation ***@***.***> Cc: 1191620 ***@***.***>, Author ***@***.***> Subject: Re: [Mehrancd/TsallisBrainSegmentation] problem related to use module (Issue #1) you can download the module and add it to 3D Slicer-->Edit-->Application Settings-->Modules, then add the path of the module to "Additional module paths" and restart. It will appear somewhere in module lists in Example. The module needs tensorflow, scikit,.... that automatically installs them. if you receive an error, push apply again might solve it. if you need a fast processing, you should increase the voxel size using "resample scaler volume" tool. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#1 (comment)", "url": "#1 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

[Mehrancd]

you can go to Code and download Zip and later unzip it some where. If you can not see the Code, probably you are not sign in to Github.

[1191620]

thanks a lot for your complete answer. I follow your instruction and restart program but it is not available in my extension list and modules. where can I find it ?

[Mehrancd]

No problem. probably you add only upper folder. Try to add the folder contains TsallisBrainSegmentation.py into setting->module. Then you will find it in:

You can also search through the module using:

[1191620]

thanks a lot. I could install and run it properly.
But now I am encounter with an error and while I watched the instruction video in youtube it has not been solved.

and when I ignore it , the program does not do expected results.

[1191620]

I am really appreciate for time that you dedicate to answer my questions.

[Mehrancd]

No problem. I will be happy if i can help. well, the image that you selected is not a good example. better to use T1 image like:

At first step, you need to create a label for the whole brain. Therefore, you need only to use the first part to extract a label like:

Then you can use the second part to segment brain to 3 materials as WM, GM and CSF. Therefore, you need to set brain mask and set new label for brain segmentation and press apply. it may takes several minutes (till 45 minutes) depends on resolution and PC.

[1191620]

Great. It works properly . But now my problem is related to export in as an stl file.
I have checked segmentation module in order to export but it is not available and its related icons are closed .
then I build a surface model in Model Maker module but it also can not export.
not that : I want to export model tp IA_FEmesh and mesh it .
I am really thankful if you can help me in this step too.

[Mehrancd]

Great. It is a little tricky to export a label as stl but very easy. just import the label inside "Segment Editor" using Segmentation->Import/Export nodes.

Then select Import and Labelmap and select the label in Input node and then press Import.

Then again go to "Segmentation" this time select "Export to file". there is stl and obj if you want to save one or multi color.
Good luck

[1191620]

That was perfect. you are the best . thanks a lot.