COMMIT 2: Dictionary does not have the same geometry as the dataset

[kwunh]

Hello there,

I am wondering if someone could please help me with this?

I am trying out COMMIT/COMMIT2 on my neonatal dataset. I ran through the tutorial with no issues but when I try on my own dataset, I run into this error:

IndexError: index 426006 is out of bounds for axis 0 with size 426000

This is from attempting to load the dict:

commit_dict = os.path.join(commit_dir, 'COMMIT')
mit.load_dictionary( commit_dict )

I noticed the warning:

Loading the data structure                                                 
 WARNING  Dictionary does not have the same geometry as the dataset        
   * Segments from the tracts:                                                                                                                                  
      - 94292 fibers and 7832274 segments
   * Segments from the peaks:                                                                                                                                   
      - 0 segments
   * Isotropic contributions:                                                                                                                                   
      - 150773 voxels
   * Post-processing   

So I presume something went wrong with constructing the dictionary.

I did also notice additional warnings in the earlier steps.

when running dice_connectome_build, i get:
WARNING Number of non-connecting streamlines 5708

when running dice_tractogram_sort, i get:
WARNING Some streamlines of the input tractogram are 'non-connecting'

It might just be something really obvious but I am happy to post the full tracebacks/commands I used if that helps!

Thank you,

Kai

[fullbat]

Hi Kai,

Indeed, it would be helpful if you post the commands run and the full traceback.

Not connecting streamlines when building the connectome or sorting the tractogram is quite common, so I'd rather focus on the creation of the dictionaries.

Thanks,

Matteo