NeMo v2.1.1

Freezing version v2.1a8 that has been stable. Changes since v2.1a7 include:

• Created a 91k subject-specific parcellation for the HCP MSMAll 32k_fs_LR space
• Had to modify website and main code to allow specifying ALL rois 1-91282 are filled, even if zeros
• now if atlas_list.json contains "regioncount" field, fill zeros for any missing in 1-regioncount
  (otherwise just include the unique non-zero values in input parcellation)
• also move accum+continuous options to "live" upload_internal page
• add cifti capability to chacovol_to_nifti.py
• Disable disable pairwise checkbox on website for res < 3mm (but allow override on upload_internal website)

v2.1.1 DOI: 10.5281/zenodo.11106578

NeMo v2.1

This version includes major bugfixes for both regional and pairwise outputs. The main effect of the bug was a downward shift in the scale of the regional Change in Connectivity (ChaCo) scores, which represent percent of disconnected streamlines per gray matter region. The magnitude of the shift in scale will depend on the atlas used, lesion mask patterns and the outputs requested when a user initially ran their lesion masks through the old version of the tool (pairwise, voxel-wise, regional etc). In our testing, new and old outputs were highly correlated, between 0.95 and 0.99 depending on lesion location, extent, and atlas selection, but may differ more in certain cases.

We also added new features for dilating atlases, which allows more streamline endpoints to be captured. The default behavior of many tractography tools is to expand gray-matter target ROIs to catch streamlines that end before reaching beyond white-matter. Previous NeMo outputs dilated gray-matter ROIs by 1mm. The new version allows users to choose between 0-3mm of dilation. We kept 1mm as the default for subject-specific gray matter parcellations (eg: fs86subj), and 0mm for MNI-defined parcellations (eg: AAL) for consistency with previous behavior, but users may find 2 or 3mm dilation better matches standard healthy subject connectome estimates.

In addition, when computing region-wise ChaCo scores, we now EXCLUDE all streamlines that start and end in the same region, as these are quite numerous and may not represent real underlying tracts. However, for a lobe-wise atlas or other atlas with very large regions (e.g. Yeo 7 or 17 functional networks), we recommend selecting the option to keep these streamlines. If users select both "pairwise" and "all reference subject" options upon lesion mask submission, they can re-compute region-wise outputs with or without these self-connections using the new "chacoconn_allref_to_chacovol.py" script.