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[DOC] Update FLAMEO documentation and references. #1961

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Apr 21, 2017
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[DOC] Update FLAMEO documentation and references. #1961

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e2591e9
Merge remote-tracking branch 'nipy/master'
tsalo Apr 20, 2017
0aa65d8
Reorg FLAMEO example for readability and add FLAME references.
tsalo Apr 20, 2017
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39 changes: 31 additions & 8 deletions nipype/interfaces/fsl/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
from ... import LooseVersion
from ...utils.filemanip import list_to_filename, filename_to_list
from ...utils.misc import human_order_sorted
from ...external.due import BibTeX
from ..base import (load_template, File, traits, isdefined,
TraitedSpec, BaseInterface, Directory,
InputMultiPath, OutputMultiPath,
Expand Down Expand Up @@ -931,14 +932,14 @@ class FLAMEO(FSLCommand):
Initialize FLAMEO with no options, assigning them when calling run:

>>> from nipype.interfaces import fsl
>>> import os
>>> flameo = fsl.FLAMEO(cope_file='cope.nii.gz', \
var_cope_file='varcope.nii.gz', \
cov_split_file='cov_split.mat', \
design_file='design.mat', \
t_con_file='design.con', \
mask_file='mask.nii', \
run_mode='fe')
>>> flameo = fsl.FLAMEO()
>>> flameo.inputs.cope_file = 'cope.nii.gz'
>>> flameo.inputs.var_cope_file = 'varcope.nii.gz'
>>> flameo.inputs.cov_split_file = 'cov_split.mat'
>>> flameo.inputs.design_file = 'design.mat'
>>> flameo.inputs.t_con_file = 'design.con'
>>> flameo.inputs.mask_file = 'mask.nii'
>>> flameo.inputs.run_mode = 'fe'
>>> flameo.cmdline # doctest: +ALLOW_UNICODE
'flameo --copefile=cope.nii.gz --covsplitfile=cov_split.mat --designfile=design.mat --ld=stats --maskfile=mask.nii --runmode=fe --tcontrastsfile=design.con --varcopefile=varcope.nii.gz'

Expand All @@ -948,6 +949,28 @@ class FLAMEO(FSLCommand):
input_spec = FLAMEOInputSpec
output_spec = FLAMEOOutputSpec

references_ = [{'entry': BibTeX('@article{BeckmannJenkinsonSmith2003,'
'author={C.F. Beckmann, M. Jenkinson, and S.M. Smith},'
'title={General multilevel linear modeling for group analysis in FMRI.},'
'journal={NeuroImage},'
'volume={20},'
'pages={1052-1063},'
'year={2003},'
'}'),
'tags': ['method'],
},
{'entry': BibTeX('@article{WoolrichBehrensBeckmannJenkinsonSmith2004,'
'author={M.W. Woolrich, T.E. Behrens, '
'C.F. Beckmann, M. Jenkinson, and S.M. Smith},'
'title={Multilevel linear modelling for FMRI group analysis using Bayesian inference.},'
'journal={NeuroImage},'
'volume={21},'
'pages={1732-1747},'
'year={2004},'
'}'),
'tags': ['method'],
}]

# ohinds: 2010-04-06
def _run_interface(self, runtime):
log_dir = self.inputs.log_dir
Expand Down