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)