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pmacsANTsPyNet

Framework for running ANTsPyNet tools on the PMACS LPC.

Basic usage

  runANTsXNet.sh -v <antspynet version> [-B src:dest,src:dest,...] runscript [runscript_options]

Containers

Place containers inside the containers/ directory. The script will look for containers/antspynet-[version]-with-data.sif, and the user must specify the version at run time.

Run scripts

A custom script can be run by providing the path to the script, or use one of the supported scripts listed below. Run with -h to get help, eg:

runANTsXNet.sh -v latest brain_extraction -h

The supported scripts are:

  • brain_extraction - calls the deep learning brain extraction.
  • brain_segmentation - calls deep Atropos, with customizable preprocessing
  • cerebellum_morphology - cerebellum labeling
  • cortical_thickness - calls the cortical thickness script, and saves results in a format similar to the antsCorticalThickness.sh pipeline in ANTs.
  • desikan_killiany_tourville_labeling - cortical labeling
  • hippocampal_segmentation - "deep flash" hippocampal segmentation
  • lesion_segmentation - lesion segmentation on T1w
  • mri_super_resolution - MRI super resolution, increases spatial resolution by a factor of two.
  • whole_head_inpainting - inpainting of masked lesions on T1w (FLAIR to be added)