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142 lines (71 loc) · 3.59 KB
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from bips.workflows.base import get_config
uuid = '7757e3168af611e1b9d5001e4fb1404c'
c = get_config(uuid)
"""surf_dir : Freesurfer subjects directory"""
c.surf_dir = '/mindhive/xnat/surfaces/GATES'
"""compcor_select : The first value in the list corresponds to applying t-compcor, and the second value to a-compcor. Note: both can be true"""
c.compcor_select = (True, True)
"""crash_dir : Location to store crash files"""
c.crash_dir = '/mindhive/scratch/jsalva/preproc_betaseries_bips'
"""fwhm : Full width at half max. The data will be smoothed at all values specified in this list."""
c.fwhm = [0.0, 5.0]
"""sink_dir : Location where the BIP will store the results"""
c.sink_dir = '/mindhive/gablab/GATES/Analysis/preproc_betaseries_bips'
"""reg_params : None"""
c.reg_params = (True, True, True, True, True)
"""use_fieldmap : True to include fieldmap distortion correction. Note: field_dir must be specified"""
c.use_fieldmap = False
"""z_thresh : z thresh for art"""
c.z_thresh = 3.0
"""magnitude_template : None"""
c.magnitude_template = '%s/magnitude.nii.gz'
"""TR : TR of functional"""
c.TR = 2.0
"""field_dir : Base directory of field-map data (Should be subject-independent) Set this value to None if you don't want fieldmap distortion correction"""
c.field_dir = ''
"""working_dir : Location of the Nipype working directory"""
c.working_dir = '/mindhive/scratch/jsalva/preproc_betaseries_bips'
"""subjects : Subject id's. Note: These MUST match the subject id's in the Freesurfer directory. For simplicity, the subject id's should also match with the location of individual functional files."""
c.subjects = ['300', '301', '302', '303', '304', '305', '306', '307', '308', '309', '310', '311', '312', '313', '314', '315']
"""SliceOrder : None"""
c.SliceOrder = ''
"""hpcutoff : highpass cutoff"""
c.hpcutoff = 128.0
"""plugin_args : Plugin arguments."""
c.plugin_args = {'qsub_args': '-q many'}
"""Interleaved : True for Interleaved"""
c.Interleaved = False
"""test_mode : Affects whether where and if the workflow keeps its intermediary files. True to keep intermediary files. """
c.test_mode = False
"""num_noise_components : number of principle components of the noise to use"""
c.num_noise_components = 6
"""phase_template : None"""
c.phase_template = '%s/phase.nii.gz'
"""TE_diff : difference in B0 field map TEs"""
c.TE_diff = 0.0
"""do_slicetiming : Perform slice timing correction"""
c.do_slicetiming = False
"""run_using_plugin : True to run pipeline with plugin, False to run serially"""
c.run_using_plugin = True
"""echospacing : EPI echo spacing"""
c.echospacing = 0.0
"""json_sink : Location to store json_files"""
c.json_sink = '/mindhive/gablab/GATES/Analysis/preproc_betaseries_bips'
"""norm_thresh : norm thresh for art"""
c.norm_thresh = 1.0
"""plugin : plugin to use, if run_using_plugin=True"""
c.plugin = 'PBS'
"""use_advanced_options : None"""
c.use_advanced_options = False
"""lowpass_freq : None"""
c.lowpass_freq = 1.0
"""base_dir : Base directory of data. (Should be subject-independent)"""
c.base_dir = '/mindhive/gablab/GATES/data'
"""sigma : 2D spatial gaussing smoothing stdev (default = 2mm)"""
c.sigma = 2
"""highpass_freq : None"""
c.highpass_freq = 0.0079
"""func_template : None"""
c.func_template = '%s/niftis/WM1.nii'
"""advanced_script : None"""
c.advanced_script = """ """