Hi Folks,
I have installed MIPAV-v-5.0.0 and the TOADS-CRUISE tools on a 64-bit machine running redhat 5.
I was trying to use lesionToads on a pair of T1-weighted and T2-weighted images. The images are in nifti format.
I am able to complete all of the installation steps as listed on the MediaWiki.
I am facing the following issues:

1. When I try to use the LesionToads plugin, the processing bar shows up and then I get the error message "Segmentation: source image locked" followed by a "Run-time exception:null"
2. When I try to use the TOADS_2008 plugin, the processing bar shows up and it says Initialization and gets upto 20% but does not complete the processing.

Any suggestions on how I may be able to able to resolve the issues listed above
Thanks
Mehul

SUBJECT: TOADS_2008 plugin

Hello,

I am running the TOADS_2008 plugin on MIPAV-v-5.1.1. The processing bar stops at 'Initialization (60%)' and then an error, 'Runtime Exception:null' appears and the process stops. Have tried with a few other versions of MIPAV and I get the same error. I am on a 64-bit Linux machine. I posted in response to the above because the issue sounded similar, was it resolved?

Any help will be very appreciated!

Thanks,
Agatha

Hi Everyone,
I have installed MIPAV 5.1.1 and the TOADS-CRUISE tools on a 32 bit maching runing Ubuntu.
I have also been trying to run lesionToads, on a pair of T1 and FLAIR images, in nifti format.

I am faced with very similar issues to both Mehul and Agatha, in that when I run both TOADS_2008 and lesionToads, the processing bar stops at Initilization 60%,and will not continue.

Any help would be much appreciated.
Kind Regards
Todd

One partial solution is to increase the RAM for MIPAV.
We had to increase it to the max limit and we got it to run.
However, we had another issue too. We are trying to segment lesions
using T1 (1*1*1) and T2 (0.5*0.5*3) images.
We are not able to get a good result yet. It might be that we did not address the difference in image resolution appropriately. Will post a message once we make progress.

I have recently tried to increase RAM for MIPAV to try and get the segmentation to work. However, I am still unable to get the segmentation to work even after allocating 3900Mb for MIPAV.
Unlike the problem I was having before where it freezes at Initialization 60%, I am getting the same Runtime Exception: Null error as Agatha.
Is this still a problem with not enough RAM? If so how much do I need to allocate to MIPAV? Or is this a problem with the plugin itself and is there another version of the plugin that I could try?
Thanks
Todd

Hi Todd,

When you got 'Runtime Exception: Null', check the line above it to see if you also got 'Java heap space' error. This would mean the issue is not enough RAM. Try the maximum amount of RAM - 6GB if you can. I ended purchasing more memory as my 4GB RAM +2GB swap wasn't going to do it. And I'm pretty sure there is no other version of this plugin..

Will post a response once my memory gets in!

Agatha

Re: RAM; I run MIPAV under MAC OS 10.5.8 on a MAC PRO 8-core (1st gen) that came with 8GB or RAM.
While trying to run TOADS with 6 GB allocated to MIPAV the system would hang at the 60% INIT as reported by others.
I just installed an extra 8GB of RAM today and can report that while allocating 12 GB to MIPAV (out of the now 16 GB) it went fine.
While monitoring memory usage, I could see the program taking upwards of 7.5 GB, so 6 GB might not cut it and 8 might be the magic number.

- Olivier
Originally posted by Agatha Monzon:

Hi Mehul,

The input images should have the same resolution. You should first register T2 image to T1 image and then input them to Lesion-TOADS. The images should also be skull stripped. I hope this solve your problem. On the memory issue, Lesion-TOADS requires about 8 GB.

-Navid