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RF: update objects with niworkflows #6

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Feb 6, 2020
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RF: update objects with niworkflows #6

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a71a394
rf: reflect Space changes
mgxd Feb 5, 2020
2f0e92d
RF: port over new methods, update smriprep pin
mgxd Feb 6, 2020
666ee2d
fix: fs outputs
mgxd Feb 6, 2020
3dcce68
doc: bad import
mgxd Feb 6, 2020
814aa45
apply suggestions from code review
mgxd Feb 6, 2020
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16 changes: 10 additions & 6 deletions docs/spaces.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@ onto other output spaces.
That is achieved using the ``--output-spaces`` argument, where standard and
nonstandard spaces can be inserted.

.. important::
*fMRIPrep* will reduce the amount of output spaces to just spaces listed in ``--output-spaces``,
even if other options require resampling the preprocessed data into intermediary spaces.

Standard spaces
"""""""""""""""
When using *fMRIPrep* in a workflow that will investigate effects that span across
Expand Down Expand Up @@ -151,18 +155,18 @@ To do so, follow the next steps.
created in ``$HOME/.cache/templateflow``.
You can modify such a configuration with the ``TEMPLATEFLOW_HOME``
environment variable, e.g.::

$ export TEMPLATEFLOW_HOME=$HOME/.templateflow

2. Install the client within your favorite Python 3 environment (this can
be done in your login-node, or in a host with Internet access,
be done in your login-node, or in a host with Internet access,
without need for Docker/Singularity)::

$ python -m pip install -U templateflow

3. Use the ``get()`` utility of the client to pull down all the templates you'll
want to use. For example::

$ python -c "from templateflow.api import get; get(['MNI152NLin2009cAsym', 'MNI152NLin6Asym', 'OASIS30ANTs', 'MNIPediatricAsym', 'MNIInfant'])"

After pulling down the resources you'll need, you will just need to make sure your
Expand Down
53 changes: 22 additions & 31 deletions docs/workflows.rst
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Expand Up @@ -19,17 +19,9 @@ is presented below:
:simple_form: yes

from collections import namedtuple
from niworkflows.utils.spaces import Space
from fmriprep.utils.spaces import SpacesManager
from niworkflows.utils.spaces import Reference, SpatialReferences
from fmriprep.workflows.base import init_single_subject_wf
BIDSLayout = namedtuple('BIDSLayout', ['root'])
spaces = SpacesManager([
('MNI152Lin', {}),
('fsaverage', {'density': '10k'}),
('T1w', {}),
('fsnative', {})
])
spaces.snap()
BIDSLayout = namedtuple('BIDSLayout', ('root'))
wf = init_single_subject_wf(
anat_only=False,
aroma_melodic_dim=-200,
Expand Down Expand Up @@ -57,8 +49,13 @@ is presented below:
regressors_dvars_th=1.5,
regressors_fd_th=0.5,
skull_strip_fixed_seed=False,
skull_strip_template=Space('OASIS30ANTs', {}),
spaces=spaces,
skull_strip_template=Reference('OASIS30ANTs'),
spaces=SpatialReferences(
spaces=[('MNI152Lin', {}),
('fsaverage', {'density': '10k'}),
('T1w', {}),
('fsnative', {})],
checkpoint=True),
subject_id='test',
t2s_coreg=False,
task_id='',
Expand All @@ -75,7 +72,7 @@ T1w/T2w preprocessing
:graph2use: orig
:simple_form: yes

from niworkflows.utils.spaces import Space, SpatialReferences
from niworkflows.utils.spaces import Reference, SpatialReferences
from fmriprep.workflows.anatomical import init_anat_preproc_wf
wf = init_anat_preproc_wf(
bids_root='.',
Expand All @@ -85,7 +82,7 @@ T1w/T2w preprocessing
num_t1w=1,
omp_nthreads=1,
output_dir='.',
skull_strip_template=Space('MNI152NLin2009cAsym', {}),
skull_strip_template=Reference('MNI152NLin2009cAsym'),
spaces=SpatialReferences([
('MNI152Lin', {}),
('fsaverage', {'density': '10k'}),
Expand Down Expand Up @@ -291,16 +288,8 @@ BOLD preprocessing
:simple_form: yes

from collections import namedtuple
from niworkflows.utils.spaces import Space
from fmriprep.utils.spaces import SpacesManager
from niworkflows.utils.spaces import SpatialReferences
from fmriprep.workflows.bold.base import init_func_preproc_wf
spaces = SpacesManager([
('MNI152Lin', {}),
('fsaverage', {'density': '10k'}),
('T1w', {}),
('fsnative', {})
])
spaces.snap()
BIDSLayout = namedtuple('BIDSLayout', ['root'])
wf = init_func_preproc_wf(
aroma_melodic_dim=-200,
Expand All @@ -324,7 +313,12 @@ BOLD preprocessing
regressors_dvars_th=1.5,
reportlets_dir='.',
t2s_coreg=False,
spaces=spaces,
spaces=SpatialReferences(
spaces=[('MNI152Lin', {}),
('fsaverage', {'density': '10k'}),
('T1w', {}),
('fsnative', {})],
checkpoint=True),
use_aroma=False,
use_bbr=True,
use_syn=True,
Expand Down Expand Up @@ -506,18 +500,15 @@ Resampling BOLD runs onto standard spaces
:graph2use: colored
:simple_form: yes

from fmriprep.utils.spaces import SpacesManager
from niworkflows.utils.spaces import SpatialReferences
from fmriprep.workflows.bold import init_bold_std_trans_wf
spaces = SpacesManager([
('MNI152Lin', {}),
('MNIPediatricAsym', {'cohort': '6'}),
])
spaces.snap()
wf = init_bold_std_trans_wf(
freesurfer=True,
mem_gb=3,
omp_nthreads=1,
spaces=spaces,
spaces=SpatialReferences(
spaces=[('MNI152Lin', {}), ('MNIPediatricAsym', {'cohort': '6'})],
checkpoint=True),
)

This sub-workflow concatenates the transforms calculated upstream (see
Expand Down
12 changes: 6 additions & 6 deletions fmriprep/cli/run.py
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Expand Up @@ -38,7 +38,7 @@ def get_parser():
from packaging.version import Version
from ..__about__ import __version__
from .version import check_latest, is_flagged
from ..utils.spaces import Space, SpacesManager, SpacesManagerAction
from niworkflows.utils.spaces import Reference, SpatialReferences, OutputReferencesAction

verstr = 'fMRIPrep v{}'.format(__version__)
currentv = Version(__version__)
Expand Down Expand Up @@ -123,7 +123,7 @@ def get_parser():
'option is not enabled, standard EPI-T1 coregistration is performed '
'using the middle echo.')
g_conf.add_argument(
'--output-spaces', nargs='+', action=SpacesManagerAction, default=SpacesManager(),
'--output-spaces', nargs='+', action=OutputReferencesAction, default=SpatialReferences(),
help="""\
Standard and non-standard spaces to resample anatomical and functional images to. \
Standard spaces may be specified by the form \
Expand Down Expand Up @@ -182,7 +182,7 @@ def get_parser():
# ANTs options
g_ants = parser.add_argument_group('Specific options for ANTs registrations')
g_ants.add_argument(
'--skull-strip-template', action='store', default='OASIS30ANTs', type=Space.from_string,
'--skull-strip-template', default='OASIS30ANTs', type=Reference.from_string,
help='select a template for skull-stripping with antsBrainExtraction')
g_ants.add_argument('--skull-strip-fixed-seed', action='store_true',
help='do not use a random seed for skull-stripping - will ensure '
Expand Down Expand Up @@ -693,7 +693,7 @@ def parse_spaces(opts):

"""
spaces = opts.output_spaces
spaces.snap()
spaces.checkpoint()

if opts.use_aroma:
# Make sure there's a normalization to FSL for AROMA to use.
Expand All @@ -706,15 +706,15 @@ def parse_spaces(opts):
spaces.add(('MNI152NLin6Asym', {'res': vol_res}))

# These arguments implicitly signal expected output
if not spaces.spaces:
if not spaces.references:
warnings.warn(
"fMRIPrep will not generate preprocessed derivatives because "
"none of `--output-spaces`, `--use-aroma`, or `--cifti-output` "
"were set."
)

# Add the default standard space (required by several sub-workflows)
if "MNI152NLin2009cAsym" not in spaces.get_std_spaces(dim=(3,)):
if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
spaces.add("MNI152NLin2009cAsym")
return spaces

Expand Down
59 changes: 0 additions & 59 deletions fmriprep/utils/spaces.py
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81 changes: 37 additions & 44 deletions fmriprep/workflows/base.py
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Expand Up @@ -85,17 +85,9 @@ def init_fmriprep_wf(
from collections import namedtuple, OrderedDict
BIDSLayout = namedtuple('BIDSLayout', ['root'])
from fmriprep.workflows.base import init_fmriprep_wf
from niworkflows.utils.spaces import Space
from fmriprep.utils.spaces import SpacesManager
from niworkflows.utils.spaces import Reference, SpatialReferences

os.environ['FREESURFER_HOME'] = os.getcwd()
spaces = SpacesManager([
('MNI152Lin',),
('fsaverage', {'density': '10k'}),
('T1w',),
('fsnative',)
])
spaces.snap()
wf = init_fmriprep_wf(
anat_only=False,
aroma_melodic_dim=-200,
Expand Down Expand Up @@ -123,8 +115,13 @@ def init_fmriprep_wf(
regressors_fd_th=0.5,
run_uuid='X',
skull_strip_fixed_seed=False,
skull_strip_template=Space('OASIS30ANTs', {}),
spaces=spaces,
skull_strip_template=Reference('OASIS30ANTs'),
spaces=SpatialReferences(
spaces=['MNI152Lin',
('fsaverage', {'density': '10k'}),
'T1w',
'fsnative'],
checkpoint=True),
subject_list=['fmripreptest'],
t2s_coreg=False,
task_id='',
Expand Down Expand Up @@ -191,15 +188,15 @@ def init_fmriprep_wf(
skull_strip_fixed_seed : bool
Do not use a random seed for skull-stripping - will ensure
run-to-run replicability when used with --omp-nthreads 1
spaces : :py:class:`~fmriprep.utils.spaces.SpacesManager`
Organize and filter spatial normalizations. Composed of internal and output lists
of spaces in the form of (Template, Specs). `Template` is a string of either
TemplateFlow IDs (e.g., ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNI152NLin2009cAsym``, or
``fsLR``), nonstandard references (e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.),
or paths pointing to custom templates organized in a TemplateFlow-like structure.
Specs is a dictionary with template specifications (e.g., the specs for the template
``MNI152Lin`` could be ``{'resolution': 2}`` if one wants the resampling to be done on
the 2mm resolution version of the selected template).
spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences`
A container for storing, organizing, and parsing spatial normalizations. Composed of
:py:class:`~niworkflows.utils.spaces.Reference` objects representing spatial references.
Each ``Reference`` contains a space, which is a string of either TemplateFlow template IDs
(e.g., ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNIPediatricAsym``), nonstandard references
(e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.), or a custom template located in
the TemplateFlow root directory. Each ``Reference`` may also contain a spec, which is a
dictionary with template specifications (e.g., a specification of ``{'resolution': 2}``
would lead to resampling on a 2mm resolution of the space).
subject_list : list
List of subject labels
t2s_coreg : bool
Expand Down Expand Up @@ -336,18 +333,10 @@ def init_single_subject_wf(
:simple_form: yes

from collections import namedtuple
from niworkflows.utils.spaces import Space
from fmriprep.utils.spaces import SpacesManager
from niworkflows.utils.spaces import Reference, SpatialReferences
from fmriprep.workflows.base import init_single_subject_wf

BIDSLayout = namedtuple('BIDSLayout', ['root'])
spaces = SpacesManager([
('MNI152Lin',),
('fsaverage', {'density': '10k'}),
('T1w',),
('fsnative',)
])
spaces.snap()
wf = init_single_subject_wf(
anat_only=False,
aroma_melodic_dim=-200,
Expand Down Expand Up @@ -375,8 +364,13 @@ def init_single_subject_wf(
regressors_dvars_th=1.5,
regressors_fd_th=0.5,
skull_strip_fixed_seed=False,
skull_strip_template=Space('OASIS30ANTs', {}),
spaces=spaces,
skull_strip_template=Reference('OASIS30ANTs'),
spaces=SpatialReferences(
spaces=['MNI152Lin',
('fsaverage', {'density': '10k'}),
'T1w',
'fsnative'],
checkpoint=True),
subject_id='test',
t2s_coreg=False,
task_id='',
Expand Down Expand Up @@ -450,15 +444,15 @@ def init_single_subject_wf(
List of subject labels
t2s_coreg : bool
For multi-echo EPI, use the calculated T2*-map for T2*-driven coregistration
spaces : :py:class:`~fmriprep.utils.spaces.SpacesManager`
Organize and filter spatial normalizations. Composed of internal and output lists
of spaces in the form of (Template, Specs). `Template` is a string of either
TemplateFlow IDs (e.g., ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNI152NLin2009cAsym``, or
``fsLR``), nonstandard references (e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.),
or paths pointing to custom templates organized in a TemplateFlow-like structure.
Specs is a dictionary with template specifications (e.g., the specs for the template
``MNI152Lin`` could be ``{'resolution': 2}`` if one wants the resampling to be done on
the 2mm resolution version of the selected template).
spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences`
A container for storing, organizing, and parsing spatial normalizations. Composed of
:py:class:`~niworkflows.utils.spaces.Reference` objects representing spatial references.
Each ``Reference`` contains a space, which is a string of either TemplateFlow template IDs
(e.g., ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNIPediatricAsym``), nonstandard references
(e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.), or a custom template located in
the TemplateFlow root directory. Each ``Reference`` may also contain a spec, which is a
dictionary with template specifications (e.g., a specification of ``{'resolution': 2}``
would lead to resampling on a 2mm resolution of the space).
task_id : str or None
Task ID of BOLD series to preprocess, or ``None`` to preprocess all
use_aroma : bool
Expand Down Expand Up @@ -536,10 +530,9 @@ def init_single_subject_wf(
bids_info = pe.Node(BIDSInfo(
bids_dir=layout.root, bids_validate=False), name='bids_info')

summary = pe.Node(SubjectSummary(
std_spaces=spaces.get_std_spaces(),
nstd_spaces=spaces.get_nonstd_spaces()),
name='summary', run_without_submitting=True)
summary = pe.Node(SubjectSummary(std_spaces=spaces.get_spaces(nonstandard=False),
nstd_spaces=spaces.get_spaces(standard=False)),
name='summary', run_without_submitting=True)

about = pe.Node(AboutSummary(version=__version__,
command=' '.join(sys.argv)),
Expand Down
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