FastSurfer_test.py

import os
import typing as ty
import pydra  
from pydra import Workflow, mark
from pydra.engine.specs import File
from pydra.tasks.fastsurfer.latest import fastsurfer
from fileformats.generic import File, Directory
from fileformats.medimage import NiftiGzXBvec, NiftiGz
from pathlib import Path

# Define the path and output_path variables
path = '/Users/arkievdsouza/Documents/NIFdata/ds000114'
output_path = '/Users/arkievdsouza/git/t1-pipeline/working-dir'

# Define the input_spec for the workflow
input_spec = {"t1w": NiftiGz, "fs_license": File, "sub_ID": str}
# output_spec = ["output_FS"]  # : Directory}
output_spec = {"output_FS": Directory}

# Create a workflow 
wf = Workflow(name='FastSurferTest', input_spec=input_spec, cache_dir=output_path, output_spec=output_spec) 

# FastSurfer Task
wf.add(
    fastsurfer(
        T1_files=wf.lzin.t1w, 
        fs_license=wf.lzin.fs_license,
        subject_id=wf.lzin.sub_ID,
        threads=7,
        parallel=True,
        name="FastSurfer_task",
        seg_only=True,
        py="python3.11",
        no_cuda=True
        # container_info=('docker','deepmi/fastsurfer:latest')
    )    

)

wf.set_output(("output_FS", wf.FastSurfer_task.lzout.subjects_dir))

# Execute the workflow
result = wf(
    t1w="/Users/arkievdsouza/Documents/NIFdata/ds000114/sub-01/ses-retest/anat/sub-01_ses-retest_T1w.nii.gz",
    fs_license="/Users/arkievdsouza/Desktop/FastSurferTesting/ReferenceFiles/FS_license.txt",
    sub_ID="sub-01_ses-retest",
    plugin="serial"
)

# print(f"Processed output generated at '{result.output.dwi_preproc}'")

# create_dotfile