5ttgen: [ERROR] FSL FIRST has failed; only 8 of 10 structures were segmented successfully

1

Dear MRtrix3 community, In following situation what should I do?

first.logs files are like this

  • first_flirt.o*
    • initial registration 0
    • Stage 2: use subcortical mask
  • first.o.*.3
    • create shapeModel
    • done creating shapeModel
    • create shapeModel
    • done creating shapeModel
    • 0.972065 -0.00486445 -0.00375321
    • 0.006287 0.890024 -0.136965
    • 0.00616292 0.188574 0.8689
    • NEw done imodes transform
    • done registering model
    • mode 175.662
    • 0.972065 -0.00486445 -0.00375321
    • 0.006287 0.890024 -0.136965
    • 0.00616292 0.188574 0.8689
    • NEw done imodes transform
    • D
    • 336 2910 2910 336
    • open file first-L_Caud_first.vtk to save.
    • succesfully opened file first-L_Caud_first.vtk to save.

System is Windows 11, Ubuntu 22.04 (WSL)

image
image1888×307 30 KB

Edit = In a priot dataset 5ttgen worked fine in my setup, but for this specific data it does not work. And also same data and same 5ttgen function worked on another device with Mac setup which belongs to my fellow.

I dont understand why when setup and dataset changed function gave error.

2

This is what I got after run_first_all command, I dont understand what is the problem

image
image1895×890 52.4 KB

3

These are some other log files of first.logs

What should I do in this situation. Images are not that large (100mb for T1.nii.gz), and my UbuntuWSL has 8gb of RAM.

image
image

4

Hi, I have the same problem. Have you solved it?

5

Yes,

8 gb was not enough for my case. I increased proportion of RAM for my Ubuntu by wslconfig file.

Print htop in your Ubuntu and watch your ram performance untill function is killed to verify your problem is with RAM