func_processing.resources.ashs package

Submodules

func_processing.resources.ashs.hipseg module

Run ASHS to segment hippocampal subfields.

func_processing.resources.ashs.hipseg.run_ashs(t1_dir, t2_dir, deriv_dir, work_dir, atlas_dir, sing_img, subj, t1_file, t2_file, atlas_str)

Run automatic hippocampal subfield segmentation.

Use singularity image of docker://nmuncy/ashs to generate HC subfield labels. Relevant output copied from work_dir to deriv_dir.

Parameters

  • t1_dir (str) – absolute path to directory containing T1-weighted file

  • t2_dir (str) – absolute path to directory containing T2-weighted file

  • deriv_dir (str) – absolute path to desired output location

  • work_dir (str) – absolute path to desired working directory, relevant files are copied to deriv_dir

  • atlas_dir (str) – absolute path to directory containing ASHS atlas

  • sing_img (str) – /path/to/ashs_singularity.simg

  • subj (str) – BIDs subject (sub-1234)

  • t1_file (str) – file name of T1-weighted file (sub-1234_ses-S1_T1w.nii.gz)

  • t2_file (str) – file name of T2-weighted file (sub-1234_ses-S1_T2w.nii.gz)

  • atlas_str (str) – ASHS atlas directory, found within atlas_dir (ashs_atlas_magdeburg)

Raises

FileNotFoundError – If ASHS is run but files are not detected in work_dir/final.

Returns

final ASHS files

Return type

list

Module contents