@@ -425,6 +425,8 @@ class execution(_Config):
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"""Select a particular task from all available in the dataset."""
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templateflow_home = _templateflow_home
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"""The root folder of the TemplateFlow client."""
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+ unique_labels = None
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+ """Combinations of subject + session identifiers to be preprocessed."""
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work_dir = Path ("work" ).absolute ()
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"""Path to a working directory where intermediate results will be available."""
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write_graph = False
@@ -581,8 +583,6 @@ class workflow(_Config):
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instance keeping standard and nonstandard spaces."""
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surface_recon_method = "infantfs"
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"""Method to use for surface reconstruction."""
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- topup_max_vols = 5
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- """Maximum number of volumes to use with TOPUP, per-series (EPI or BOLD)."""
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use_aroma = None
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"""Run ICA-:abbr:`AROMA (automatic removal of motion artifacts)`."""
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use_bbr = False
@@ -694,7 +694,6 @@ def load(filename, skip=None):
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section = getattr (sys .modules [__name__ ], sectionname )
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ignore = skip .get (sectionname )
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section .load (configs , ignore = ignore )
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- init_spaces ()
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def get (flat = False ):
@@ -729,42 +728,6 @@ def to_filename(filename):
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filename .write_text (dumps ())
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- def init_spaces (checkpoint = True ):
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- """Initialize the :attr:`~workflow.spaces` setting."""
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- from niworkflows .utils .spaces import Reference , SpatialReferences
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-
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- spaces = execution .output_spaces or SpatialReferences ()
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- if not isinstance (spaces , SpatialReferences ):
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- spaces = SpatialReferences (
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- [ref for s in spaces .split (" " ) for ref in Reference .from_string (s )]
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- )
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-
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- if checkpoint and not spaces .is_cached ():
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- spaces .checkpoint ()
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-
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- # Ensure user-defined spatial references for outputs are correctly parsed.
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- # Certain options require normalization to a space not explicitly defined by users.
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- # These spaces will not be included in the final outputs.
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- if workflow .use_aroma :
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- # Make sure there's a normalization to FSL for AROMA to use.
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- spaces .add (Reference ("MNI152NLin6Asym" , {"res" : "2" }))
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-
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- if workflow .cifti_output :
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- # CIFTI grayordinates to corresponding FSL-MNI resolutions.
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- vol_res = "2" if workflow .cifti_output == "91k" else "1"
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- spaces .add (Reference ("fsaverage" , {"den" : "164k" }))
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- spaces .add (Reference ("MNI152NLin6Asym" , {"res" : vol_res }))
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- # Ensure a non-native version of MNIInfant is added as a target
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- if workflow .age_months is not None :
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- from .utils .misc import cohort_by_months
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-
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- cohort = cohort_by_months ("MNIInfant" , workflow .age_months )
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- spaces .add (Reference ("MNIInfant" , {"cohort" : cohort }))
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-
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- # Make the SpatialReferences object available
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- workflow .spaces = spaces
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-
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-
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def _process_initializer (cwd , omp_nthreads ):
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"""Initialize the environment of the child process."""
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os .chdir (cwd )
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