NITRC TumorSim Forum: help

hwo to creat the initial tuomr (seed)

Saeid Ghazanfari Shabankareh — Tue, 01 Nov 2022 11:42:08 GMT

Hello every one,

I am using the Tumorsim, but I don't know how to create initial tumor for the program. how can I build a initial tumor for use the program?

Thanks for your helping

Help: Generating Full Tumor Image

Ahmed Alastal — Wed, 19 Oct 2016 12:41:02 GMT

Hello,
I'm new to this, and I'd like to know How can I Generate Full brain Tumor Image from the output dataset

Thanks

TumorSIm running on macos

Auxiliadora Sarmiento — Tue, 19 Jul 2016 13:14:11 GMT

It is possible to run Tumosim in Macos Yosemite?

TumorSimInput missing Flair_1.mha

Mohammad Havaei — Thu, 04 Jun 2015 13:44:01 GMT

Im trying to use the TumorSim package. I downloaded the TumorSimInput folder and got the tumorseed from another file (which had the same space as modalities in TumorSimInput) when I run the xml file it says that it can not find the flair_1.mha in the texture folder

Do I need to copy it from some where?
Thanks

RE: how to generate a tumor-free image?

Tom Haeck — Mon, 22 Sep 2014 7:03:59 GMT

Hey Xiaoxiao,

sorry for my late reply!
The tissue probabilities are part of the input that is provided to the simulator, i.e. p_csf.mha, p_white.mha, p_grey, ...
You need to multiply each one of these probabilities with the corresponding texture image and add the results of the multiplications.
Multiplication and addition of images can easily be done with any program where you have straight access to the image values, e.g. Matlab.

Greetings,

Tom

RE: how to generate a tumor-free image?

Xiaoxiao Liu — Mon, 08 Sep 2014 18:01:40 GMT

Hi Tom,
Thanks for the quick reply.
Did you try the recipe yourself using TumorSim? or some other programs you wrote?

In order to match up with the tumor-containing images (generated from the default parameters provided in the xml file), I need to know the tissue probabilities that were used? Where I should look for those numbers?
Thank you.

-Best,
Xiaoxiao

RE: how to generate a tumor-free image?

Tom Haeck — Mon, 08 Sep 2014 7:06:35 GMT

Hey,

Maybe you can have a look at Marcel Prastawa's answer from January 13th, 2014:
[url=forum.php?thread_id=4249&forum_id=2386]http://www.nitrc.org/forum/forum.php?thread_id=4249&forum_id=2386[/url]
In this post, it is suggested to create a 'healthy' MR-image by making a linear combination of the input probabilities and the input textures that you use for generating the tumor image.

Good luck,

Tom

how to generate a tumor-free image?

Xiaoxiao Liu — Mon, 08 Sep 2014 5:06:19 GMT

Hi there,
I am trying to generate some tumor-free FLAIR images using TumorSim.
(The goal is to generate some ground truth healthy MRI data to compare with the corresponding
images with tumors.) Look like the program expects a "correct" tumor seed to work
(I try to cheat the program with an empty seed, but without luck. It gave the warning about the
bad seed and crashed after running for a little while ).

I am wondering is there a simple way that I could skip the step of "planting" tumors into the image?
Thanks a lot!

-best,
Xiaoxiao

RE: How to install and use

Tom Haeck — Fri, 07 Mar 2014 14:31:02 GMT

Hey all,

Answers regarding the MSVCP110.dll - problem are provided on:
https://www.nitrc.org/forum/forum.php?thread_id=3745&forum_id=2386

As for now, there is not a lot of documentation available. You can use the example *.xml files on the website. The filename of the *.xml-files needs to be parsed as a parameter to Tumorsim, e.g. execute on the command line: tumorsim1.2.2_win64.exe parameter_file.xml

Regards,

Tom

RE: How to install and use

Miguel Yanez — Fri, 07 Mar 2014 1:39:51 GMT

Hi, I have the same question. If you find the way to install the program please tell me. Thanks