Closed sebastientourbier closed 2 years ago
Custom
option for segmentation_tool
custom_bids_derivatives
that specifyies the BIDS derivatives directory where WM tissue and brain masks are locatedpybids_config
a path to a JSON file that specifies the pybids
query to get the WM mask (like label-WM
)Custom Parcellation
option for parcellation_scheme
custom_bids_derivatives
that specifyies the BIDS derivatives directory where parcellation(s) is(are) locatedpybids_config
a path to a JSON file that specifies the pybids
query to get the atlas (like atlas=Desikan
)parcellation_name
the name of the atlas used in the output parcellation filename of the anatomical pipeline.
Brainstorming on how to make CMP3 handling custom cortical parcellation atlases.
Possible inputs
Custom BIDS derivative directory with parcellation in native space - (_atlas-_dseg.nii.gz and _atlas-_dseg.tsv) i.e.:
following the BIDS specs as described in https://bids-specification.readthedocs.io/en/stable/05-derivatives/03-imaging.html#common-image-derived-labels.
Freesurfer .annot files like:
Freesurfer .gcs (like the brainnetome atlas - https://atlas.brainnetome.org/)
Resources