update docs, add doctests

Author: josephmje

dmriprep/__about__.py

@@ -5,13 +5,13 @@
 __version__ = get_versions()['version']
 del get_versions
 
-__packagename__ = "dmriprep"
-__credits__ = ("Contributors: please check the ``.zenodo.json`` file at the"
-               "top-level folder of the repository")
-__url__ = "https://github.com/nipy/dmriprep"
+__packagename__ = 'dmriprep'
+__credits__ = ('Contributors: please check the ``.zenodo.json`` file at the'
+               'top-level folder of the repository')
+__url__ = 'https://github.com/nipy/dmriprep'
 
 DOWNLOAD_URL = (
-    "https://github.com/nipy/dmriprep/{name}/archive/{ver}.tar.gz".format(
+    'https://github.com/nipy/dmriprep/{name}/archive/{ver}.tar.gz'.format(
         name=__packagename__, ver=__version__
     )
 )

dmriprep/__init__.py

@@ -13,5 +13,5 @@
 
 # Filter warnings that are visible whenever you import another package that
 # was compiled against an older numpy than is installed.
-warnings.filterwarnings("ignore", message="numpy.dtype size changed")
-warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
+warnings.filterwarnings('ignore', message='numpy.dtype size changed')
+warnings.filterwarnings('ignore', message='numpy.ufunc size changed')

dmriprep/cli.py

@@ -13,114 +13,114 @@
 
 # Filter warnings that are visible whenever you import another package that
 # was compiled against an older numpy than is installed.
-warnings.filterwarnings("ignore", message="numpy.dtype size changed")
-warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
+warnings.filterwarnings('ignore', message='numpy.dtype size changed')
+warnings.filterwarnings('ignore', message='numpy.ufunc size changed')
 
 @click.command()
 # arguments as specified by BIDS-Apps
-@click.argument("bids_dir", type=click.Path(exists=True, file_okay=False))
+@click.argument('bids_dir', type=click.Path(exists=True, file_okay=False))
 @click.argument(
-    "output_dir", type=click.Path(exists=True, file_okay=False, writable=True)
+    'output_dir', type=click.Path(exists=True, file_okay=False, writable=True)
 )
 @click.argument(
-    "analysis_level", default="participant", type=click.Choice(["participant", "group"])
+    'analysis_level', default='participant', type=click.Choice(['participant', 'group'])
 )
 # optional arguments
 # options for filtering BIDS queries
 @click.option(
-    "--skip_bids_validation",
-    help="Assume the input dataset is BIDS compliant and skip the validation",
+    '--skip_bids_validation',
+    help='Assume the input dataset is BIDS compliant and skip the validation',
     is_flag=True
 )
 @click.option(
-    "--participant_label",
+    '--participant_label',
     default=None,
-    help="The label(s) of the participant(s) that should be "
-    "analyzed. The label corresponds to "
-    "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."
+    help='The label(s) of the participant(s) that should be '
+    'analyzed. The label corresponds to '
+    '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.'
 )
 # options for prepping dwi scans
-# @click.option(
-#     "--concat_shells",
-#     default=None,
-#     help="A space delimited list of acq-<label>",
-# )
 @click.option(
-    "--b0_thresh",
+    '--concat_dwis',
+    default=None,
+    help='A space delimited list of acq-<label>',
+)
+@click.option(
+    '--b0_thresh',
     default=5,
     show_default=True,
-    help="Threshold for b0 value",
+    help='Threshold for b0 value',
     type=click.IntRange(min=0, max=10),
 )
 @click.option(
-    "--output_resolution",
-    help="The isotropic voxel size in mm the data will be resampled to before eddy.",
+    '--output_resolution',
+    help='The isotropic voxel size in mm the data will be resampled to before eddy.',
     type=float,
     multiple=True
 )
 # specific options for eddy
 @click.option(
-    "--omp_nthreads",
+    '--omp_nthreads',
     default=1,
     show_default=True,
-    help="Maximum number of threads for eddy",
+    help='Maximum number of threads for eddy',
     type=int,
 )
 @click.option(
-    "--eddy_niter",
+    '--eddy_niter',
     default=5,
     show_default=True,
-    help="Fixed number of eddy iterations. See "
-    "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide"
-    "#A--niter",
+    help='Fixed number of eddy iterations. See '
+    'https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide'
+    '#A--niter',
     type=int,
 )
 @click.option(
-    "--bet_dwi",
+    '--bet_dwi',
     default=0.3,
     show_default=True,
-    help="Fractional intensity threshold for BET on the DWI. "
-    "A higher value will be more strict; it will cut off more "
-    "around what it analyzes the brain to be.",
+    help='Fractional intensity threshold for BET on the DWI. '
+    'A higher value will be more strict; it will cut off more '
+    'around what it analyzes the brain to be.',
     type=click.FloatRange(min=0, max=1),
 )
 @click.option(
-    "--bet_mag",
+    '--bet_mag',
     default=0.3,
     show_default=True,
-    help="Fractional intensity threshold for BET on the magnitude. "
-    "A higher value will be more strict; it will cut off more "
-    "around what it analyzes the brain to be.",
+    help='Fractional intensity threshold for BET on the magnitude. '
+    'A higher value will be more strict; it will cut off more '
+    'around what it analyzes the brain to be.',
     type=click.FloatRange(min=0, max=1),
 )
 @click.option(
-    "--acqp_file",
+    '--acqp_file',
     default=None,
-    help="If you want to pass in an acqp file for topup/eddy instead of"
-    "generating it from the json by default.",
+    help='If you want to pass in an acqp file for topup/eddy instead of'
+    'generating it from the json by default.',
     type=click.Path(exists=True, dir_okay=False),
 )
 # workflow configuration
 @click.option(
-    "--ignore",
-    "-i",
-    help="Specify which node(s) to skip during the preprocessing of the dwi.",
-    type=click.Choice(["denoise", "unring"]),
+    '--ignore',
+    '-i',
+    help='Specify which node(s) to skip during the preprocessing of the dwi.',
+    type=click.Choice(['denoise', 'unring', 'fieldmaps']),
     multiple=True,
 )
 @click.option(
-    "--work_dir",
-    "-w",
-    help="working directory",
+    '--work_dir',
+    '-w',
+    help='working directory',
     type=click.Path(exists=True, file_okay=False, writable=True),
 )
 @click.option(
-    "--synb0_dir",
+    '--synb0_dir',
     default=None,
-    help="If you want to use Synb0-DISCO for preprocessing.",
+    help='If you want to use Synb0-DISCO for preprocessing.',
     type=click.Path(exists=True, file_okay=False),
 )
 def main(
@@ -131,6 +131,7 @@ def main(
     skip_bids_validation,
     work_dir,
     ignore,
+    concat_dwis,
     b0_thresh,
     output_resolution,
     bet_dwi,
@@ -152,10 +153,10 @@ def main(
     participant level analyses can be run independently (in parallel).
     """
 
-    if analysis_level != "participant":
+    if analysis_level != 'participant':
         raise NotImplementedError(
-            "The only valid analysis level for dmriprep "
-            "is participant at the moment."
+            'The only valid analysis level for dmriprep '
+            'is participant at the moment.'
         )
 
     layout = BIDSLayout(bids_dir, validate=True)
@@ -169,7 +170,7 @@ def main(
         validate_input_dir(bids_dir, all_subjects, subject_list)
 
     if not work_dir:
-        work_dir = os.path.join(output_dir, "scratch")
+        work_dir = os.path.join(output_dir, 'scratch')
 
     if len(output_resolution) == 1:
         output_resolution = output_resolution * 3
@@ -180,6 +181,7 @@ def main(
         output_dir=output_dir,
         work_dir=work_dir,
         ignore=list(ignore),
+        concat_dwis=list(concat_dwis),
         b0_thresh=b0_thresh,
         output_resolution=output_resolution,
         bet_dwi=bet_dwi,
@@ -188,13 +190,13 @@ def main(
         synb0_dir=synb0_dir
     )
     wf.write_graph()
-    wf.config["execution"]["remove_unnecessary_outputs"] = False
-    wf.config["execution"]["keep_inputs"] = True
-    wf.config["execution"]["crashfile_format"] = "txt"
+    wf.config['execution']['remove_unnecessary_outputs'] = False
+    wf.config['execution']['keep_inputs'] = True
+    wf.config['execution']['crashfile_format'] = 'txt'
     wf.run()
 
     return 0
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     sys.exit(main())  # pragma: no cover

dmriprep/data/boilerplate.bib

@@ -123,66 +123,32 @@ @article{flirt
     pages = {143--156}
 }
 
-@article{mcflirt,
-    author = {Jenkinson, Mark and Bannister, Peter and Brady, Michael and Smith, Stephen},
-    doi = {10.1006/nimg.2002.1132},
-    issn = {1053-8119},
+@article{denoise1,
+    title = {Denoising of diffusion MRI using random matrix theory},
+    volume = {142},
+    doi = {10.1016/j.neuroimage.2016.08.016},
     journal = {NeuroImage},
-    number = 2,
-    pages = {825-841},
-    title = {Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images},
-    url = {http://www.sciencedirect.com/science/article/pii/S1053811902911328},
-    volume = 17,
-    year = 2002
+    author = {Veraart, J.; Novikov, D.S.; Christiaens, D.; Ades-aron, B.; Sijbers, J. & Fieremans, E.},
+    year = {2016},
+    pages = {394-406}
 }
 
-@article{bbr,
-    author = {Greve, Douglas N and Fischl, Bruce},
-    doi = {10.1016/j.neuroimage.2009.06.060},
-    issn = {1095-9572},
-    journal = {NeuroImage},
-    number = 1,
-    pages = {63-72},
-    title = {Accurate and robust brain image alignment using boundary-based registration},
-    volume = 48,
-    year = 2009
+@article{denoise2,
+    title = {Diffusion MRI noise mapping using random matrix theory},
+    volume = {76},
+    doi = {10.1002/mrm.26059},
+    journal = {Magnetic Resonance in Medicine},
+    author = {Veraart, J.; Fieremans, E. & Novikov, D.S.},
+    year = {2016},
+    pages = {1582-1593}
 }
 
-@article{power_fd_dvars,
-    author = {Power, Jonathan D. and Mitra, Anish and Laumann, Timothy O. and Snyder, Abraham Z. and Schlaggar, Bradley L. and Petersen, Steven E.},
-    doi = {10.1016/j.neuroimage.2013.08.048},
-    issn = {1053-8119},
-    journal = {NeuroImage},
-    number = {Supplement C},
-    pages = {320-341},
-    title = {Methods to detect, characterize, and remove motion artifact in resting state fMRI},
-    url = {http://www.sciencedirect.com/science/article/pii/S1053811913009117},
-    volume = 84,
-    year = 2014
-}
-
-@article{confounds_satterthwaite_2013,
-    author = {Satterthwaite, Theodore D. and Elliott, Mark A. and Gerraty, Raphael T. and Ruparel, Kosha and Loughead, James and Calkins, Monica E. and Eickhoff, Simon B. and Hakonarson, Hakon and Gur, Ruben C. and Gur, Raquel E. and Wolf, Daniel H.},
-    doi = {10.1016/j.neuroimage.2012.08.052},
-    issn = {10538119},
-    journal = {NeuroImage},
-    number = 1,
-    pages = {240--256},
-    title = {{An improved framework for confound regression and filtering for control of motion artifact in the preprocessing of resting-state functional connectivity data}},
-    url = {http://linkinghub.elsevier.com/retrieve/pii/S1053811912008609},
-    volume = 64,
-    year = 2013
-}
-
-@article{hcppipelines,
-    author = {Glasser, Matthew F. and Sotiropoulos, Stamatios N. and Wilson, J. Anthony and Coalson, Timothy S. and Fischl, Bruce and Andersson, Jesper L. and Xu, Junqian and Jbabdi, Saad and Webster, Matthew and Polimeni, Jonathan R. and Van Essen, David C. and Jenkinson, Mark},
-    doi = {10.1016/j.neuroimage.2013.04.127},
-    issn = {1053-8119},
-    journal = {NeuroImage},
-    pages = {105-124},
-    series = {Mapping the Connectome},
-    title = {The minimal preprocessing pipelines for the Human Connectome Project},
-    url = {http://www.sciencedirect.com/science/article/pii/S1053811913005053},
-    volume = 80,
-    year = 2013
+@article{unring,
+    title = {Gibbs-ringing artifact removal based on local subvoxel-shifts},
+    volume = {76},
+    doi = {10.1002/mrm.26054},
+    journal = {Magnetic Resonance in Medicine},
+    author = {Kellner, E; Dhital, B; Kiselev, V.G & Reisert, M.},
+    year = {2016},
+    pages = {1574–1581}
 }