diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py index 9462b71a52..9fc3696f9a 100644 --- a/nipype/interfaces/afni/base.py +++ b/nipype/interfaces/afni/base.py @@ -3,7 +3,7 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: """Provide interface to AFNI commands.""" from __future__ import print_function, division, unicode_literals, absolute_import -from builtins import object, str, bytes +from builtins import object, str from future.utils import raise_from import os @@ -13,6 +13,7 @@ from ...utils.filemanip import split_filename from ..base import ( CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec) +from ...external.due import BibTeX # Use nipype's logging system IFLOGGER = logging.getLogger('interface') @@ -148,6 +149,32 @@ class AFNICommand(AFNICommandBase): input_spec = AFNICommandInputSpec _outputtype = None + references_ = [{'entry': BibTeX('@article{Cox1996,' + 'author={R.W. Cox},' + 'title={AFNI: software for analysis and ' + 'visualization of functional magnetic ' + 'resonance neuroimages},' + 'journal={Computers and Biomedical research},' + 'volume={29},' + 'number={3},' + 'pages={162-173},' + 'year={1996},' + '}'), + 'tags': ['implementation'], + }, + {'entry': BibTeX('@article{CoxHyde1997,' + 'author={R.W. Cox and J.S. Hyde},' + 'title={Software tools for analysis and ' + 'visualization of fMRI data},' + 'journal={NMR in Biomedicine},' + 'volume={10},' + 'number={45},' + 'pages={171-178},' + 'year={1997},' + '}'), + 'tags': ['implementation'], + }] + def __init__(self, **inputs): super(AFNICommand, self).__init__(**inputs) self.inputs.on_trait_change(self._output_update, 'outputtype') diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index d622a2866a..cb544a7e46 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -24,6 +24,7 @@ from ..base import ( CommandLineInputSpec, CommandLine, Directory, TraitedSpec, traits, isdefined, File, InputMultiPath, Undefined, Str) +from ...external.due import BibTeX from .base import ( AFNICommandBase, AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec) @@ -694,6 +695,16 @@ class FWHMx(AFNICommandBase): _cmd = '3dFWHMx' input_spec = FWHMxInputSpec output_spec = FWHMxOutputSpec + + references_ = [{'entry': BibTeX('@article{CoxReynoldsTaylor2016,' + 'author={R.W. Cox, R.C. Reynolds, and P.A. Taylor},' + 'title={AFNI and clustering: false positive rates redux},' + 'journal={bioRxiv},' + 'year={2016},' + '}'), + 'tags': ['method'], + }, + ] _acf = True def _parse_inputs(self, skip=None): diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 62ea7851ac..dc60f2c816 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1387,8 +1387,8 @@ def _get_ram_mb(pid, pyfunc=False): def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): """Function to get the RAM and threads usage of a process - Paramters - --------- + Parameters + ---------- pid : integer the process ID of process to profile mem_mb : float diff --git a/nipype/interfaces/fsl/base.py b/nipype/interfaces/fsl/base.py index e1280e1130..f5353f2b06 100644 --- a/nipype/interfaces/fsl/base.py +++ b/nipype/interfaces/fsl/base.py @@ -34,6 +34,7 @@ from ... import logging from ...utils.filemanip import fname_presuffix from ..base import traits, isdefined, CommandLine, CommandLineInputSpec +from ...external.due import BibTeX LOGGER = logging.getLogger('interface') @@ -157,6 +158,18 @@ class FSLCommand(CommandLine): input_spec = FSLCommandInputSpec _output_type = None + references_ = [{'entry': BibTeX('@article{JenkinsonBeckmannBehrensWoolrichSmith2012,' + 'author={M. Jenkinson, C.F. Beckmann, T.E. Behrens, ' + 'M.W. Woolrich, and S.M. Smith},' + 'title={FSL},' + 'journal={NeuroImage},' + 'volume={62},' + 'pages={782-790},' + 'year={2012},' + '}'), + 'tags': ['implementation'], + }] + def __init__(self, **inputs): super(FSLCommand, self).__init__(**inputs) self.inputs.on_trait_change(self._output_update, 'output_type')