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Add duecredit citations for FSL, AFNI, 3dFWHMx.
Also fix small type in interfaces/base.py.
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-2
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4 files changed

+83
-2
lines changed

‎nipype/interfaces/afni/base.py

Lines changed: 28 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""Provide interface to AFNI commands."""
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from __future__ import print_function, division, unicode_literals, absolute_import
6-
from builtins import object, str, bytes
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from builtins import object, str
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from future.utils import raise_from
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import os
@@ -13,6 +13,7 @@
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from ...utils.filemanip import split_filename
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from ..base import (
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CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec)
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from ...external.due import BibTeX
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# Use nipype's logging system
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IFLOGGER = logging.getLogger('interface')
@@ -148,6 +149,32 @@ class AFNICommand(AFNICommandBase):
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input_spec = AFNICommandInputSpec
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_outputtype = None
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152+
references_ = [{'entry': BibTeX('@article{Cox1996,'
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'author={R.W. Cox},'
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'title={AFNI: software for analysis and '
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'visualization of functional magnetic '
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'resonance neuroimages},'
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'journal={Computers and Biomedical research},'
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'volume={29},'
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'number={3},'
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'pages={162-173},'
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'year={1996},'
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'}'),
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'tags': ['implementation'],
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},
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{'entry': BibTeX('@article{CoxHyde1997,'
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'author={R.W. Cox and J.S. Hyde},'
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'title={Software tools for analysis and '
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'visualization of fMRI data},'
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'journal={NMR in Biomedicine},'
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'volume={10},'
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'number={45},'
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'pages={171-178},'
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'year={1997},'
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'}'),
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'tags': ['implementation'],
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}]
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def __init__(self, **inputs):
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super(AFNICommand, self).__init__(**inputs)
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self.inputs.on_trait_change(self._output_update, 'outputtype')

‎nipype/interfaces/afni/utils.py

Lines changed: 11 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@
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from ..base import (
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CommandLineInputSpec, CommandLine, Directory, TraitedSpec,
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traits, isdefined, File, InputMultiPath, Undefined, Str)
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from ...external.due import BibTeX
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from .base import (
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AFNICommandBase, AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec)
@@ -694,6 +695,16 @@ class FWHMx(AFNICommandBase):
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_cmd = '3dFWHMx'
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input_spec = FWHMxInputSpec
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output_spec = FWHMxOutputSpec
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references_ = [{'entry': BibTeX('@article{CoxReynoldsTaylor2016,'
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'author={R.W. Cox, R.C. Reynolds, and P.A. Taylor},'
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'title={AFNI and clustering: false positive rates redux},'
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'journal={bioRxiv},'
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'year={2016},'
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'}'),
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'tags': ['method'],
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},
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]
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_acf = True
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def _parse_inputs(self, skip=None):

‎nipype/interfaces/base.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1387,7 +1387,7 @@ def _get_ram_mb(pid, pyfunc=False):
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def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False):
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"""Function to get the RAM and threads usage of a process
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1390-
Paramters
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Parameters
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---------
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pid : integer
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the process ID of process to profile

‎nipype/interfaces/fsl/base.py

Lines changed: 43 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -34,6 +34,7 @@
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from ... import logging
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from ...utils.filemanip import fname_presuffix
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from ..base import traits, isdefined, CommandLine, CommandLineInputSpec
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from ...external.due import BibTeX
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LOGGER = logging.getLogger('interface')
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@@ -157,6 +158,48 @@ class FSLCommand(CommandLine):
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input_spec = FSLCommandInputSpec
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_output_type = None
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references_ = [{'entry': BibTeX('@article{WoolrichJbabdiPatenaudeChappellMakniBehrens'
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'BeckmannJenkinsonSmith2009,'
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'author={M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, '
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'S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, and S.M. Smith},'
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'title={Bayesian analysis of neuroimaging data in FSL},'
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'journal={NeuroImage},'
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'volume={45},'
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'number={1},'
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'pages={S173-186},'
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'year={2009},'
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'}'),
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'tags': ['implementation'],
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},
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{'entry': BibTeX('@article{SmithJenkinsonWoolrichBeckmannBehrensJohansen'
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'BergBannisterDeLucaDrobnjakFlitneyNiazySaundersVickers'
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'ZhangDeStefanoBradyMatthews2004,'
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'author={S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, '
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'T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, '
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'I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, '
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'Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews},'
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'title={Advances in functional and structural MR image analysis '
182+
'and implementation as FSL},'
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'journal={NeuroImage},'
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'volume={23},'
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'number={S1},'
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'pages={208-219},'
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'year={2004},'
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'}'),
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'tags': ['implementation'],
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},
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{'entry': BibTeX('@article{JenkinsonBeckmannBehrensWoolrichSmith2012,'
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'author={M. Jenkinson, C.F. Beckmann, T.E. Behrens, '
193+
'M.W. Woolrich, and S.M. Smith},'
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'title={FSL},'
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'journal={NeuroImage},'
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'volume={62},'
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'pages={782-790},'
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'year={2012},'
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'}'),
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'tags': ['implementation'],
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}]
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160203
def __init__(self, **inputs):
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super(FSLCommand, self).__init__(**inputs)
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self.inputs.on_trait_change(self._output_update, 'output_type')

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