Hello,

I tried to use the newest version of autoseg (from github)
and run into the following problem

AutoSeg -gui crashes and the log files shows the following messages?

unknown line:Is AuxT1 Image: 0
unknown line:Is AuxT2 Image: 0
unknown line:Is AuxPD Image: 0
unknown line:Is Aux1 Image: 0
unknown line:Is Aux2 Image: 0
unknown line:Is Aux3 Image: 0
unknown line:Is Aux4 Image: 0
unknown line:Is Aux5 Image: 0
unknown line:Is Aux6 Image: 0
unknown line:Is Aux7 Image: 0
unknown line:Is Aux8 Image: 0
number of data: 1
setting multiAtlas Directory
No such EM Software (itkEMS no longer supported)!
size of data: 2
size of data: /home/andi/proj_mridata/mprage.nii
Tissue Atlas: /home/andi/proj_autoseg/tools/atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/
Stripped Tissue Atlas: /tools/atlas/BrainsegAtlas/adult-atlas-asym-stripped-T1-RAI/
number of Tissues: 4
Error EM Software (itkEMS is no longer supported)!

Can anyone give a hint how to solve this problem?

Thank you
Andi

Hello Andi,

Thank you for using Autoseg. I am guessing you successfully built it from the source code that you found on github. Autoseg is a software that creates a pipeline to run other tools. Therefore it needs the other tools to run correctly. Unfortunately, I don't think there is currently a list for the users that specifies which tools are needed and where to find them. Most tools can be built are part of the AutoSeg build. You just have to select "ON" when you configure your project with cmake for each of them. I am currently in the process of verifying that all the necessary tools are actually compilable from AutoSeg's project, and I will try to improve a little bit the install process such that all the tools can be installed in one final install directoty. I will keep you posted when this is done.

Francois

Hello Andi,

I have actually spotted a few bugs that lead to this message. I have corrected them in version 3.2.0. Let me know if this solves your issue.
Basically, the problem was that under certain circonstances, some parameters were not initialized. That lead the tool to think it was using an old segmentation method (itkEMS) that was not supported anymore, thus the message.