Dear Dr. Iglesias,

I'm a researcher at the University of Minho - ICSV Institute, conducting research on hippocampal patterns in Alzheimer's disease. I've used NextBrain for detailed hippocampal and full segmentation on NACC dataset subjects.

Issue:

I noticed your NextBrain demo website shows hippocampal structures including:

prosubiculum (uncal, rostral, caudal)

presubiculum (rostral, caudal)

indusium_griseum

supracallosal_subiculum

However, these structures don't appear in either atlas_simplified or atlas_full YAML configuration files in FreeSurfer 8.1. I've verified this by checking:

data_simplified/atlas_names_and_labels.yaml

data_full/atlas_names_and_labels.yaml

Additionally, when attempting to use atlas_full, the segmentation crashes with "IndexError: list index out of range" at label 266, suggesting the data_full/combined_atlas_labels_1mm.yaml config is incomplete (maps only 265 of 334 labels).

Questions:

Are these additional hippocampal subfields available in FreeSurfer dev or a more recent atlas version?

If not yet released, are they planned for a future update?

Would you recommend an alternative approach for segmenting these specific structures?

Should I post these issues in the official FreeSurfer GitHub repository for broader advice ?

Note: I'm running NextBrain via FreeSurfer 8.1 Docker container, due to incompatibility issues in our workstation with the OS. The Docker image was missing both the atlas files and the Python segmentation scripts, so I had to manually download:

atlas_simplified.zip and atlas_full.zip from the FTP server
ERC_bayesian_segmentation scripts from the GitHub dev branch
SuperSynth_August_2025.pth model (1GB)

After mounting these files into the container, atlas_simplified works perfectly. However, atlas_full crashes as described above, and neither atlas contains the additional hippocampal subfields visible in your demo. From my understanding, recently (in the past week) a new version with the bayesian segmentation folder was put available but the issues I have remain.

Another small note: I had to manually correct the mri_histo_atlas_segment_fireants.sh script because some of the parameters for the python scripts where missing. I'm not sure if that's supposed to happen or if it's a version error.

Thank you for your attention. I look forward to receiving a response.

Best regards,

Luís

Researcher, Informatics Engineering

University of Minho - ICVS