NITRC TOADS-CRUISE Brain Segmentation Tools Forum: help

RE: How to download FANTASM plugin in MIPAV

p_maheta — Wed, 08 May 2024 13:23:38 GMT

<blockquote>Hi justin, I am running into several issues downloading FANTASM for MIPAV. I have installed TOADS-CRUISE and FANTASM shows up under Plugins -> TOADS-CRUISE -> Segmentation -> FANTASM. However when i click on FANTASM the toolbox the dialog box will not show up for the next steps on tissue segmentation. Am i missing a dependency/bundle  to be able to use FANTASM ? I was hoping to download the FANTASM plugin through the link on MIPAV but it can't reach the page. Would it be possible to have the files sent to my email pr663935@dal.ca?  Side note: I am not sure if this is related to this but this is what shows up in my output box under debug: DEBUG level 0: Unable to find menu item named Show Expanded Model DEBUG level 0: Unable to find menu item named Adaptive noise reduction DEBUG level 0: Unable to find menu item named Graph based DEBUG level 0: Unable to find menu item named Time series optimized automatic registration DEBUG level 0: Unable to find menu item named ActiveContours Any help would be appreciated.  Thanks, Parth</blockquote>

No output in Lesion toads

butlerj3 — Thu, 11 Oct 2018 14:43:08 GMT

Hope this reaches you well. I am attempting to run lesion toads on my desktop. I am running to an issue where no output images are being generated when I run this algorithm.

I have
input my skull stripped T1 and FLAIR images
Used the lesiontoads-12obj.txt files for the atlases
Designated that the output images should be of hard segmentation+memberships
The rest is what was provided as default settings.
Is there an issue on my end to why this is not giving the outputs I am looking for?
Could you please lend a helping hand?
Thank you

Lesion-TOADS for infratentorial MS lesions

Afsaneh Shirani — Fri, 29 Sep 2017 15:10:06 GMT

Dear All,
I was wondering if anyone has any experience or suggestions on how to improve the performance of lesion-TOADS for segmentation of "infratentorial" lesions in multiple sclerosis? I am happy with lesion-TOADS performance for "supratentorial" lesions, but not getting good results for the infratentorial ones. I would appreciate any comments.
Best,
Afsaneh

what is "atlas list" in spectre?

Hsiu-Wei Yang — Tue, 06 Jun 2017 18:06:11 GMT

Hi everyone,

I am pretty to MIPAV. while I am trying to run spectre_10, I am required to provide "atlas list".
What does "atlas list" mean? Where can get or download it?
I would really appreciate it if someone can help me out.

Thanks,
Hank

RE: Welcome to Help

baby92 — Sun, 26 Mar 2017 7:58:10 GMT

Hi,

I need HELP!
I want to use skeletonize 3D Pot algorithm of MIPAV on MRI image (nifti format) butti can't find this option. I read on web site of MIPAV that i have to go to Algorithm --> Morphological --> Skeletonize 3D Pot but i can't find tris option after i open my image.

Someone can iHELP me??

RE: Color-coding hard-segmentation in Lesion-Toad

Anikta sharma — Fri, 10 Feb 2017 1:58:30 GMT

Hi Lukasz

Would you mind sharing steps of Lesion-Toad analysis? Or can you just share a good source taht might be helpful. There is no manual for data processing?

Thanks!

Thickness

Raul Wirz — Fri, 21 Oct 2016 15:09:52 GMT

Dear,

After run LongCruise pipeline, I have two volumes with the thickness (thicknessVol and thicknesslevset).
Thicknesslevset is totally empty, a empty volume with the only value of 0.
And the other volume, Ho I can use this volume to obtain cortical thickness?

Thanks

Crash at initcentroid

Carole SUDRE — Sat, 09 Jul 2016 15:50:52 GMT

Hello,

I am trying to run Lesion-TOADS with Mipav 7.3.0 and the R4c version of TOADS-CRUISE but the process systematically crashes at the initialisation of the centroid.

Is this a known problem? How is it possible to fix it?

Many thanks in advance for your help

Kind regards

Carole

Color-coding hard-segmentation in Lesion-Toad

Uki Buki — Sun, 22 May 2016 7:29:27 GMT

Hi,

I have a really simple question that I seem unable to go past (I am an absolute beginner). I have run a Lesion-Toads in MIPAV on an MS brain so that I have now two nifti files - 1) a lesion mask, 2) hard segmentation results (I can get all volume statistics from all 25 coded regions so I assume everything went fine). The problem I have is that I would like to get the following images:

1) Color-coded hard segmentation i.e. with lesions marked in red, WH in white etc.
2) FLAIR image with lesions superimposed on it
3) 3D reconstruction of the lesions against a brain background.

PS. How can I open the .input file type?

Thank you in advance.
Lukasz

There is no Manual on 'running TOADS-CRUISE'.

Seongjin Choi — Thu, 18 Feb 2016 20:47:31 GMT

It would be great if there is a comprehensive manual for running TOADS-CRUISE.