mass updates

Author: josephmje

dmriprep/cli.py

@@ -40,13 +40,26 @@
     'sub-<participant_label> from the BIDS spec (the "sub-" '
     'prefix can be removed). If this parameter is not provided '
     'all subjects will be analyzed. Multiple participants '
-    'can be specified with a space delimited list.'
+    'can be specified with a space delimited list.',
+    multiple=True
+)
+@click.option(
+    '--session_label',
+    default=None,
+    help='The label(s) of session(s) that should be analyzed. '
+         'the label corresponds to ses-<session_label from the '
+         'BIDS spec (the "ses-" prefix can be removed). If this '
+         'parameter is not provided, all sessions will be '
+         'analyzed. Multiple sessions can be specified with '
+         'a space delimited list.',
+    multiple=True
 )
 # options for prepping dwi scans
 @click.option(
     '--concat_dwis',
     default=None,
     help='A space delimited list of acq-<label>',
+    multiple=True
 )
 @click.option(
     '--b0_thresh',
@@ -115,7 +128,7 @@
     '--ignore',
     '-i',
     help='Specify which node(s) to skip during the preprocessing of the dwi.',
-    type=click.Choice(['denoise', 'unring', 'fieldmaps']),
+    type=click.Choice(['denoising', 'unringing', 'fieldmaps']),
     multiple=True,
 )
 @click.option(
@@ -132,6 +145,7 @@
 )
 def main(
     participant_label,
+    session_label,
     bids_dir,
     output_dir,
     analysis_level,
@@ -185,6 +199,7 @@ def main(
 
     wf = init_dmriprep_wf(
         subject_list=subject_list,
+        session_list=session_label,
         layout=layout,
         output_dir=output_dir,
         work_dir=work_dir,
@@ -194,6 +209,7 @@ def main(
         output_resolution=output_resolution,
         bet_dwi=bet_dwi,
         bet_mag=bet_mag,
+        nthreads=nthreads,
         omp_nthreads=omp_nthreads,
         synb0_dir=synb0_dir
     )

dmriprep/data/boilerplate.bib

@@ -1,3 +1,15 @@
+@article{van2011numpy,
+        title={The NumPy array: a structure for efficient numerical computation},
+        author={Van Der Walt, Stefan and Colbert, S Chris and Varoquaux, Gael},
+        journal={Computing in Science \& Engineering},
+        volume={13},
+        number={2},
+        pages={22--30},
+        year={2011},
+        publisher={AIP Publishing},
+        doi={10.1109/MCSE.2011.37}
+        }
+
 @article{nipype1,
     author = {Gorgolewski, K. and Burns, C. D. and Madison, C. and Clark, D. and Halchenko, Y. O. and Waskom, M. L. and Ghosh, S.},
     doi = {10.3389/fninf.2011.00013},

dmriprep/data/eddy_parameters.json

@@ -0,0 +1,27 @@
+{
+    "flm": "quadratic",
+    "slm": "none",
+    "fwhm": 0,
+    "niter": 5,
+    "fep": false,
+    "interp": "spline",
+    "method": "jac",
+    "nvoxhp": 1000,
+    "fudge_factor": 10,
+    "dont_sep_offs_move": false,
+    "dont_peas": false,
+    "repol": true,
+    "outlier_nstd": 4,
+    "outlier_nvox": 250,
+    "outlier_type": "sw",
+    "outlier_pos": false,
+    "outlier_sqr": false,
+    "estimate_mov_by_susceptibility": false,
+    "is_shelled": false,
+    "num_threads": 1,
+    "use_cuda": false,
+    "cnr_maps": true,
+    "residuals": true,
+    "output_type": "NIFTI_GZ",
+    "args": ""
+}

dmriprep/due.py

@@ -0,0 +1,74 @@
+# emacs: at the end of the file
+# ex: set sts=4 ts=4 sw=4 et:
+# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
+"""
+
+Stub file for a guaranteed safe import of duecredit constructs:  if duecredit
+is not available.
+
+To use it, place it into your project codebase to be imported, e.g. copy as
+
+    cp stub.py /path/tomodule/module/due.py
+
+Note that it might be better to avoid naming it duecredit.py to avoid shadowing
+installed duecredit.
+
+Then use in your code as
+
+    from .due import due, Doi, BibTeX, Text
+
+See  https://github.com/duecredit/duecredit/blob/master/README.md for examples.
+
+Origin:     Originally a part of the duecredit
+Copyright:  2015-2019  DueCredit developers
+License:    BSD-2
+"""
+
+__version__ = '0.0.8'
+
+
+class InactiveDueCreditCollector(object):
+    """Just a stub at the Collector which would not do anything"""
+    def _donothing(self, *args, **kwargs):
+        """Perform no good and no bad"""
+        pass
+
+    def dcite(self, *args, **kwargs):
+        """If I could cite I would"""
+        def nondecorating_decorator(func):
+            return func
+        return nondecorating_decorator
+
+    active = False
+    activate = add = cite = dump = load = _donothing
+
+    def __repr__(self):
+        return self.__class__.__name__ + '()'
+
+
+def _donothing_func(*args, **kwargs):
+    """Perform no good and no bad"""
+    pass
+
+
+try:
+    from duecredit import due, BibTeX, Doi, Url, Text
+    if 'due' in locals() and not hasattr(due, 'cite'):
+        raise RuntimeError(
+            "Imported due lacks .cite. DueCredit is now disabled")
+except Exception as e:
+    if not isinstance(e, ImportError):
+        import logging
+        logging.getLogger("duecredit").error(
+            "Failed to import duecredit due to %s" % str(e))
+    # Initiate due stub
+    due = InactiveDueCreditCollector()
+    BibTeX = Doi = Url = Text = _donothing_func
+
+# Emacs mode definitions
+# Local Variables:
+# mode: python
+# py-indent-offset: 4
+# tab-width: 4
+# indent-tabs-mode: nil
+# End: