[BUG]: Cannot register parcellation with non-continuous values

[synchon]

Is there an existing issue for this?

• I have searched the existing issues

Current Behavior

I want to register the Glasser parcellation: https://afni.nimh.nih.gov/pub/dist/atlases/MNI_HCP/MNI_Glasser_HCP_2021_v1.0a/

However, I get this error:

  File "/home/fraimondo/dev/tbox/junifer/junifer/data/parcellations.py", line 269, in load_parcellation
    raise_error(
  File "/home/fraimondo/dev/tbox/junifer/junifer/utils/logging.py", line 289, in raise_error
    raise klass(msg)
ValueError: Parcellation Glasser must have all the values in the range  [0, 361].

This is because so far, junifer expects that parcellation values are continuous. Some parcellations are not, like this one. The values are 1-180 for one hemisphere, and 1001-1180 for the other.

This was a restriction added when merging parcellations, as we have to "shift" the values to merge them, and this is done by adding the number of labels:

junifer/junifer/data/parcellations.py

Lines 1362 to 1364 in 3fd1877

	# Increase the values of each ROI to match the labels
	t_parc_data[t_parc_data != 0] += len(labels)

Expected Behavior

Parcellations without continuous numbering should be able to be included in junifer (and merged)

Steps To Reproduce

1. Get junifer latest
2. Register the Glasser parcellation
3. Try to compute any marker that uses a parcel (or even load_parcellation)

Environment

junifer:
  version: 0.0.3.dev101
python:
  version: 3.11.3
  implementation: CPython
dependencies:
  click: 8.1.3
  numpy: 1.23.5
  datalad: 0.18.2+59.gc5054cb91
  pandas: 1.5.3
  nibabel: 4.0.2
  nilearn: 0.10.0
  sqlalchemy: 1.4.48
  ruamel.yaml: 0.17.31
system:
  platform: Linux-6.1.0-12-amd64-x86_64-with-glibc2.36
environment:
  LC_CTYPE: en_US.UTF-8
  PATH: 
    /home/fraimondo/miniconda3/envs/junifer/bin:/home/fraimondo/miniconda3/condabin:/home/fraimondo/.dotfiles/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games

Relevant log output

No response

Anything else?

No response

[github-actions]

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2025-10-07 10:47 UTC

[synchon]

CI passing on juseless.