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brainnetome_test.py
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brainnetome_test.py
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from pydra import Workflow, mark, ShellCommandTask
import os
from pydra.engine.specs import SpecInfo, BaseSpec, ShellSpec, ShellOutSpec
from pydra.tasks.freesurfer.auto import MRIsCALabel, Label2Vol, CALabel
from pydra.tasks.mrtrix3.v3_0 import mrcalc
from fileformats.generic import File
import typing as ty
# Define some filepaths
freesurfer_home='/Applications/freesurfer/'
mrtrix_lut_dir='/Users/arkievdsouza/git/mrtrix3/share/mrtrix3/labelconvert/'
output_path = '/Users/arkievdsouza/git/t1-pipeline/working-dir/brainnetome246fs_testing/'
os.environ["SUBJECTS_DIR"] = ''
# os.environ["PYTHONHASHSEED"] = ''
# Define the input values using input_spec
input_spec = {"FS_dir": str, "parcellation": str}
wf = Workflow(name='brainnetome_parcellation', input_spec=input_spec, cache_dir=output_path)
@mark.task
@mark.annotate({
"parcellation": str,
"FS_dir": str,
"freesurfer_home": str,
"return": {
"output_parcellation_filename": str,
"parc_lut_file": str,
"brainnetome_gcs_path_lh": str,
"brainnetome_gcs_path_rh": str,
"brainnetome_sgm_gca_path": str,
"lh_annotation": str,
"rh_annotation": str,
"sphere_file_lh": str,
"sphere_file_rh": str,
"cortex_label_lh": str,
"cortex_label_rh": str,
"template_volume": str,
"output_volume_l2v_lh": str,
"output_volume_l2v_rh": str,
"transform": str,
"output_volume_calabel": str,
}
})
def join_task_brainnetome(parcellation: str, FS_dir: str, freesurfer_home: str):
if parcellation == 'brainnetome246fs':
# brainnetome definitions
output_parcellation_filename = os.path.join(FS_dir,"mri","aparc.BN_Atlas+aseg.mgz")
parc_lut_file = os.path.join(freesurfer_home,'brainnetome','BN_Atlas_246_LUT.txt')
brainnetome_gcs_path_lh=os.path.join(freesurfer_home,'average','lh.BN_Atlas.gcs')
brainnetome_gcs_path_rh=os.path.join(freesurfer_home,'average','rh.BN_Atlas.gcs')
brainnetome_sgm_gca_path=os.path.join(freesurfer_home,'average','BN_Atlas_subcortex.gca')
lh_annotation= os.path.join(FS_dir,"label","lh.BN_Atlas.annot")
rh_annotation= os.path.join(FS_dir,"label","rh.BN_Atlas.annot")
sphere_file_lh=os.path.join(FS_dir,'surf','lh.sphere.reg')
sphere_file_rh=os.path.join(FS_dir,'surf','rh.sphere.reg')
cortex_label_lh=os.path.join(FS_dir,'label','lh.cortex.label')
cortex_label_rh=os.path.join(FS_dir,'label','rh.cortex.label')
template_volume=os.path.join(FS_dir,'mri','brain.mgz')
output_volume_l2v_lh=os.path.join(FS_dir,'mri','lh.BN_Atlas.mgz')
output_volume_l2v_rh=os.path.join(FS_dir,'mri','rh.BN_Atlas.mgz')
transform=os.path.join(FS_dir,'mri','transforms','talairach.m3z')
output_volume_calabel=os.path.join(FS_dir,'mri','BN_Atlas_subcortex.mgz')
return output_parcellation_filename, parc_lut_file, brainnetome_gcs_path_lh, brainnetome_gcs_path_rh,brainnetome_sgm_gca_path ,lh_annotation , rh_annotation, sphere_file_lh, sphere_file_rh, cortex_label_lh, cortex_label_rh,template_volume, output_volume_l2v_lh, output_volume_l2v_rh, transform,output_volume_calabel
wf.add(join_task_brainnetome(FS_dir=wf.lzin.FS_dir, parcellation=wf.lzin.parcellation, freesurfer_home=freesurfer_home, name="join_task"))
# ######################
# # mriS_ca_label task #
# ######################
hemispheres = ['lh', 'rh']
for hemisphere in hemispheres:
wf.add(
MRIsCALabel(
label=getattr(wf.join_task.lzout, f'cortex_label_{hemisphere}'),
subject_id=wf.lzin.FS_dir,
hemisphere=hemisphere,
canonsurf=getattr(wf.join_task.lzout, f'sphere_file_{hemisphere}'),
classifier=getattr(wf.join_task.lzout, f'brainnetome_gcs_path_{hemisphere}'),
out_file=getattr(wf.join_task.lzout, f'{hemisphere}_annotation'),
name=f'MRIsCAlabel_task_{hemisphere}'
)
)
######################
# mri_label2vol task #
######################
hemispheres = ['lh', 'rh']
for hemisphere in hemispheres:
wf.add(
Label2Vol(
annot_file=getattr(wf, f"MRIsCAlabel_task_{hemisphere}").lzout.out_file,
template_file=wf.join_task.lzout.template_volume,
vol_label_file=getattr(wf.join_task.lzout, f"output_volume_l2v_{hemisphere}"),
subject_id=wf.lzin.FS_dir,
hemi=hemisphere,
identity=True,
proj='frac 0 1 .1',
name=f'Label2Vol_task_{hemisphere}'
)
)
########################
# mri_ca_label task #
########################
wf.add(
CALabel(
in_file=wf.join_task.lzout.template_volume,
out_file=wf.join_task.lzout.output_volume_calabel,
transform=wf.join_task.lzout.transform,
template=wf.join_task.lzout.brainnetome_sgm_gca_path,
name='CALabel_task'
)
)
######################################################################
# # Need to deal with prospect of overlapping mask labels #
# - Any overlap between the two hemisphere ribbons = set to zero #
# - Any overlap between cortex and sub-cortical = retain cortex #
######################################################################
# run.command('mrcalc '
# + ' '.join([os.path.join('freesurfer',
# 'mri',
# hemi + 'h.BN_Atlas.mgz')
# for hemi in ['l', 'r']])
# + ' -mult cortex_overlap.mif'
# + ' -datatype bit')
# run.command('mrcalc '
# + ' '.join([os.path.join('freesurfer',
# 'mri',
# hemi + 'h.BN_Atlas.mgz')
# for hemi in ['l', 'r']])
# + ' -add '
# + os.path.join('freesurfer',
# 'mri',
# 'BN_Atlas_subcortex.mgz')
# + ' -mult sgm_overlap.mif'
# + ' -datatype bit')
# run.command('mrcalc '
# + ' '.join([os.path.join('freesurfer',
# 'mri',
# hemi + 'h.BN_Atlas.mgz')
# for hemi in ['l', 'r']])
# + ' -add 1.0 cortex_overlap.mif -sub -mult '
# + os.path.join('freesurfer',
# 'mri',
# 'BN_Atlas_subcortex.mgz')
# + ' 1.0 sgm_overlap.mif -sub -mult -add '
# + parc_image_path)
# app.cleanup('cortex_overlap.mif')
# app.cleanup('sgm_overlap.mif')
########################
# Execute the workflow #
########################
wf.set_output(("CALabel_task", wf.CALabel_task.lzout.out_file))
wf.set_output(("MRIsCAlabel_task_lh", wf.MRIsCAlabel_task_lh.lzout.out_file))
wf.set_output(("MRIsCAlabel_task_rh", wf.MRIsCAlabel_task_rh.lzout.out_file))
wf.set_output(("Label2Vol_task_lh", wf.Label2Vol_task_lh.lzout.vol_label_file))
wf.set_output(("Label2Vol_task_rh", wf.Label2Vol_task_rh.lzout.vol_label_file))
# wf.set_output(("cortex_overlap_task", wf.cortex_overlap_task.lzout.out_image))
result = wf(
FS_dir="/Users/arkievdsouza/git/t1-pipeline/working-dir/brainnetome246fs_testing/sub-01",
parcellation="brainnetome246fs",
plugin="serial",
)
# LH RH iterations
# # ###########################
# # # mriS_ca_label task - lh #
# # ###########################
# wf.add(
# MRIsCALabel(
# label=wf.join_task.lzout.cortex_label_lh,
# subject_id=wf.lzin.FS_dir,
# hemisphere='lh',
# canonsurf=wf.join_task.lzout.sphere_file_lh,
# classifier=wf.join_task.lzout.brainnetome_gcs_path_lh,
# out_file=wf.join_task.lzout.lh_annotation,
# name='MRIsCAlabel_task_lh'
# )
# )
# ###########################
# # mriS_ca_label task - rh #
# ###########################
# wf.add(
# MRIsCALabel(
# label=wf.join_task.lzout.cortex_label_rh,
# subject_id=wf.lzin.FS_dir,
# hemisphere='rh',
# canonsurf=wf.join_task.lzout.sphere_file_rh,
# classifier=wf.join_task.lzout.brainnetome_gcs_path_rh,
# out_file=wf.join_task.lzout.rh_annotation,
# name='MRIsCAlabel_task_rh'
# )
# )
# ###########################
# # mri_label2vol task - lh #
# ###########################
# wf.add(
# Label2Vol(
# annot_file=wf.MRIsCAlabel_task_lh.lzout.out_file,
# template_file=wf.join_task.lzout.template_volume,
# vol_label_file=wf.join_task.lzout.output_volume_l2v_lh,
# subject_id=wf.lzin.FS_dir,
# hemi='lh',
# identity=True,
# proj='frac 0 1 .1',
# name='Label2Vol_task_lh'
# )
# )
# ###########################
# # mri_label2vol task - rh #
# ###########################
# wf.add(
# Label2Vol(
# annot_file=wf.MRIsCAlabel_task_rh.lzout.out_file,
# template_file=wf.join_task.lzout.template_volume,
# vol_label_file=wf.join_task.lzout.output_volume_l2v_rh,
# subject_id=wf.lzin.FS_dir,
# hemi='rh',
# identity=True,
# proj='frac 0 1 .1',
# name='Label2Vol_task_rh'
# )
# )