import glob
from functools import partial
import numpy as np
import nipype.interfaces.io as nio # Data i/o
import nipype.interfaces.fsl as fsl # fsl
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import nipype.algorithms.modelgen as model # model generation
from nipeep import Memory
from pyxnat import Interface
mem = Memory('.')
central = Interface('https://central.xnat.org', 'schwarty', 'plopplop',
'/havoc/store/xnat')
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
input_files = [central.select('/project/Volatile/resources/123150742/files/000075760021s002a1001.nii.gz').get()]
# where put files arguments?
# extract_ref = partial(mem.cache(fsl.ExtractROI), t_min=42, t_size=1)
nosestrip = partial(mem.cache(fsl.BET), frac=0.3)
skullstrip = partial(mem.cache(fsl.BET), mask=True)
refskullstrip = partial(mem.cache(fsl.BET), mask=True)
# coregister = mem.cache(fsl.FLIRT)(dof=6)
FSL_BASE = '/usr/share/fsl/4.1'
os.environ['FSLDIR'] = FSL_BASE
os.environ['PATH'] = '%s:%s/bin' % (os.environ['PATH'], FSL_BASE)
os.environ['LD_LIBRARY_PATH'] = '%s:/usr/lib/fsl/4.1/' % (
os.environ.get('LD_LIBRARY_PATH', ''))
from nipype.interfaces import fsl
fsl.FSLCommand.set_default_output_type('NIFTI')
################################################################################
from nipeep import Memory
import glob
in_files = glob.glob(os.path.join(FSL_BASE, 'data',
'standard', 'MNI152_T1_2mm*'))
################################################################################
mem = Memory('.')
threshold = [mem.cache(fsl.Threshold)(in_file=f, thresh=i)
for i, f in enumerate(in_files)]
out_merge = mem.cache(fsl.Merge)(dimension="t",
in_files=[t.outputs.out_file for t in threshold],
)
out_mean = mem.cache(fsl.MeanImage)(in_file=out_merge.outputs.merged_file)
# Avoid having increasing disk size: keep only what was touch in this run
mem.clear_previous_runs()
#mem.clear_runs_since(year=2011)
