search

ftdc-picsl / antsnetct

Cortical thickness with ANTsPyNet
Apache License 2.0
0 stars 0 forks source link

BIDS Segmentation labels? #3

Closed cookpa closed 7 months ago

cookpa commented 9 months ago

https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#common-image-derived-labels

The BIDS common derived labels are different to ANTs:

Integer value Description Abbreviation (label) 2 White Matter WM 3 Cerebrospinal Fluid CSF 8 Cortical Gray Matter CGM 9 Subcortical Gray Matter SGM 10 Brainstem BS 11 Cerebellum CBM

We can either roll with these, or use a tsv file to correspond to standard ANTs labels.

Whatever solution we choose, it will affect both segmentations generated by the pipeline, and segmentations input to use as priors.

cookpa commented 9 months ago

Consensus on Slack seems to be to go with BIDS

cookpa commented 8 months ago

This is now implemented.

One issue is that this makes for bad visualization with ITK-SNAP default labels.

cookpa commented 8 months ago

Possible workarounds for label coloring:

  1. ITK SNAP devs could solve by setting default colors in order of existing labels, rather than 1,2,3,4,5,6.

  2. Make and share snap label definitions. Unfortunately these have to be loaded every time.

  3. ITK-SNAP could support BIDS label definitions (possible but maybe not likely given that it is not a BIDS app)

Label defs + command line aliases would work for me, but IDK about others