NITRC TOADS-CRUISE Brain Segmentation Tools Forum: open-discussion

Lesion Toads and MIPAV v8.0.2

Kyle Kern — Tue, 06 Aug 2019 21:14:28 GMT

I'm having trouble getting LesionToads to work and I'm wondering if anyone else has this problem.

I input a skull stripped T1 (in native space) and a skull stripped FLAIR aligned to the T1 (both .nii.gz format). I used the atlas file cruise-atlas-11obj-lesiontoads2009.txt for all 3 Atlas Files, because it won't let me run if I don't specify all 3. I save to a directory. It initializes and then fails during the alignment (see data output below). The progress bar goes to 20% and then closes.

I believe I've allocated enough memory (12 GB).
I'm using MIPAV v8.0.2 on a Mac OS 10.14.6.
I got the TOADS_2008 plugin to work on the same T1 image

anyone else have this issue or know how to address it?

thanks,

Kyle

Initialization
Atlas alignment
---------- Performance Summary ----------
1) Algorithm Calculation -- ELAPSED TIME: Actual: 4.62 sec / CPU: 4.52 sec

TOTAL ELAPSED TIME: Actual: 4.62 sec / CPU: 4.52 sec
CURRENT MEMORY: Used 2605 MB, Free 11769 MB, Total 14375 MB

LesionTOADS Parameter Settings, Overestimation in default settings

mvaro2002 — Fri, 08 Mar 2019 17:16:10 GMT

Dear all,

I am using LesionTOADS to calculate brain volume measures as well as Lesion Volume in MS Patients but to manual approach of the MRI I always have a significantly higher volume for Lesion Volume when running the tool. Sometimes by over 500% difference.

Does anybody have suggestions which parameters / settings should be changed to avoid this?

Thank you

Mike

LeasionTOADS Settings:

• (inAtlas) Atlas with Lesions.....
• (inOutput) Output images: Hard segmentation of lesions + sulcal CSF, filled WM and cortical GM memberships as well as filled WM mask. (CRUISE inputs).....
• (inMaximum) Maximum distance from the interventricular WM boundary to downweight the lesion membership to avoid false postives: .........
• (inMaximum2) Maximum ventricle distance: ........
• (inMaximum3) Maximum interventricular distance: .....
• (inAtlas5) Controls the effect of the statistical atlas on the segmentation: ..........
• (inSmooting) Controls the effect of neighberhood voxels on the membership: ........
• (inMaximum4) Maximum amount of relative change in the energy function considered as the convergence criteria: ........
• (inMaximum5) Maximum iterations: .....
• (inAtlas6) Atlas alignment: ......
• (inConnectivity) Connectivity (foreground,background): .......

install toads-cruise error

Jingwen Zhang — Wed, 07 Nov 2018 14:01:42 GMT

hello
when i use plugin the toads-cruise, the system show an error:"unable to load plugin:RoomListener Multiplexor$RoomMultiplexListener. To my surprise, I restart the MIPAV, i could see the option"toads-cruise" although i can't use it:I use the"Plugins > TOADS-CRUISE > Segmentation > TOADS_2008" but it can't open the window-TOADS 2008 GUI.
i don't know which step is wrong, and what should i do ?

RE: Issue Running Lesion Toads

butlerj3 — Thu, 11 Oct 2018 13:47:16 GMT

Ended up installing on the windows side of my mac, got this to run. Now running into another issue. The lesion toads plugin is running, however when it has completed I am not getting any output images.

Anyone else have this issue

Issue Running Lesion Toads

butlerj3 — Wed, 10 Oct 2018 13:41:15 GMT

i am trying to run lesion toads on a T1 and FLAIR but it doesn't seem to run, and keeps popping up with the "save as" window for the output image. any ideas how i get past this point?
i am running it on a Mac
Thanks

RE: running lesion toads

butlerj3 — Tue, 09 Oct 2018 15:11:15 GMT

[i]Originally posted by Matin Mor:[/i][quote]Hi Lesley,

I am facing the same problem. Did you manage to solve the issue? Can u please help me on this if u already have a solution? Thanks[/quote][color=#000000]I am too experiencing this issue, have you had any success in fixing this ?[/color]

RE: Atlas File - No Lesion - T1 Only

J Cuzzocreo — Tue, 13 Jun 2017 18:57:00 GMT

[color=#000000]Hi Hank,[/color]

[color=#000000]I have passed your question to a colleague who may be able to help you more quickly than I can. If not, I will take a look at this and try to help you when I get home.[/color]

[color=#000000]Jen[/color]

[i]Originally posted by Hsiu-Wei Yang:[/i][quote]Hi Jen,

please let me ask some more questions.

I can run SPECTRE after I chose a T1 image as a input, and send in "oasis-3-v2.txt" in the file you asked me to download for Atlas List.
But I can get any output result. Something wrong with system? We are supposed to get a stripped image after we finish SPECTRE?

Thanks,
Hank[/quote]

RE: Atlas File - No Lesion - T1 Only

Hsiu-Wei Yang — Tue, 13 Jun 2017 18:35:36 GMT

Hi Jen,

please let me ask some more questions.

I can run SPECTRE after I chose a T1 image as a input, and send in "oasis-3-v2.txt" in the file you asked me to download for Atlas List.
But I can get any output result. Something wrong with system? We are supposed to get a stripped image after we finish SPECTRE?

Thanks,
Hank

RE: Atlas File - No Lesion - T1 Only

J Cuzzocreo — Tue, 06 Jun 2017 18:52:33 GMT

Great! I hope SPECTRE works well for you!

Jen

RE: Atlas File - No Lesion - T1 Only

Hsiu-Wei Yang — Tue, 06 Jun 2017 18:51:27 GMT

Dear Jen,

thanks for your quick reply! I successfully download it.

Hank