Population_template problems

1

Hello!

I’m working through this pipeline and am having troubles with population_template. I’m not getting any clear errors that I can find solutions for, so I’m hoping someone can explain how to fix this:

population_template: Generating a population-average template from 16 input images
population_template: [DEBUG] commonPostfix(): Common postfix of 16 is ''
Traceback (most recent call last):
  File "/usr/local/packages/mrtrix3/bin/population_template", line 243, in <module>
    maskPrefixes.append(m.split(maskCommonPostfix)[0])
ValueError: empty separator

I’ve tried searching for the solution to ValueError and went into the source code for population_template line 243, but there isn’t anything there that seems immediately useful:

These are lines 241-243 in the source code:

  for m in maskFiles:
    maskPrefixes.append(m.split(maskCommonPostfix)[0])

For the record, I couldn’t do the symbolic linking described in step 8 because the cluster I’m working on doesn’t support it. Could this be part of the issue?

Thank you very much!

2

Hello @aszymanski

You are seeing this error because the common postfix of the mask filenames is empty. The mask images should all be in a common folder and have the same file extension.

Cheers,
Max

3

Hi Max,

Thanks for the response! To clarify, you don’t mean that the mask images should be in the same folder as the FOD images, right? Because as it is I have all mask images in a common folder with the same file extensions. Here’s an image of my setup:

image.png336×1058 88 KB

They all have .nii.gz file extensions.

Did I just make an error with my command? I’m operating from the directory which contains the template folder, which contains the mask_input and fod_input folders.

Thank you for your time :slight_smile:

4

Make sure that there are no hidden files in the mask folder.

ls -la mask_dir template/mask_input

If you can’t see anything wrong with that file list, feel free to post or send me that list.