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[WIP] ENH: Add --func-only option to skip anatomical processing #808

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[WIP] ENH: Add --func-only option to skip anatomical processing #808

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a778b21
ENH: Add --dismiss-t1w option to skip anatomical processing
Oct 16, 2017
b78a50d
Merge remote-tracking branch 'upstream/master' into madeleine-snyder-…
oesteban Oct 31, 2017
16c367a
[skip ci] Add Maddie to zenodo
oesteban Oct 31, 2017
cb3c6fc
Merge pull request #2 from oesteban/madeleine-snyder-dismiss-t1-patch
madeleinesnyder Oct 31, 2017
9fcb693
fix erroneously removed medial_surface_nan
oesteban Oct 31, 2017
db088e7
fix erroneous initialization of anatomical workflow
oesteban Oct 31, 2017
86c010e
Merge branch 'master' into func-only
oesteban Nov 1, 2017
453e91f
convert indentation to spaces
oesteban Nov 1, 2017
940340b
Connected onlyfunc workflow in workflows/base.py
Nov 1, 2017
d9b66f6
remove fmriprep/workflows/.base.py.swo
Nov 1, 2017
9b377ea
Added raise exception if user tries func_only and anat_only simultane…
Nov 1, 2017
d3decf9
Connected other workflows in workflows/bold/base.py onlyfunc
Nov 1, 2017
4878aae
Added mututally exclusive argument for func and anat in run.py
Nov 1, 2017
fc7fd68
remove .swo file, update .gitignore
oesteban Nov 13, 2017
7403a97
Merge remote-tracking branch 'upstream/master' into func-only
oesteban Nov 13, 2017
5c6fb3d
fix zenodo ordering
oesteban Nov 13, 2017
1aab4c6
Merge remote-tracking branch 'upstream/master' into func-only
oesteban Dec 7, 2017
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
# Editors
.*.py.swo

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
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4 changes: 4 additions & 0 deletions .zenodo.json
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Expand Up @@ -48,6 +48,10 @@
"affiliation": "MIT",
"orcid": "0000-0002-7252-7771"
},
{
"name": "Madeleine Snyder",
"affiliation": "Harvard Medical School, Harvard University, Cambridge, Massachusetts"
},
{
"name": "Poldrack, Russell A.",
"affiliation": "Department of Psychology, Stanford University",
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1 change: 1 addition & 0 deletions docs/workflows.rst
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Expand Up @@ -37,6 +37,7 @@ is presented below:
debug=False,
low_mem=False,
anat_only=False,
func_only=False,
hires=True,
use_bbr=True,
bold2t1w_dof=9,
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10 changes: 8 additions & 2 deletions fmriprep/cli/run.py
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Expand Up @@ -82,8 +82,7 @@ def get_parser():
'in working directory)')
g_perfm.add_argument('--use-plugin', action='store', default=None,
help='nipype plugin configuration file')
g_perfm.add_argument('--anat-only', action='store_true',
help='run anatomical workflows only')

g_perfm.add_argument('--ignore-aroma-denoising-errors', action='store_true',
default=False,
help='ignores the errors ICA_AROMA returns when there '
Expand All @@ -92,6 +91,12 @@ def get_parser():
g_perfm.add_argument("-v", "--verbose", dest="verbose_count", action="count", default=0,
help="increases log verbosity for each occurence, debug level is -vvv")

# Add mutually exclusive func_only and anat_only pipeline options
g_anatfunc = parser.add_mutually_exclusive_group()
g_anatfunc.add_argument('--anat-only', action='store_true')
g_anatfunc.add_argument('--func-only', action='store_true')

# Add workflow config arguments
g_conf = parser.add_argument_group('Workflow configuration')
g_conf.add_argument(
'--ignore', required=False, action='store', nargs="+", default=[],
Expand Down Expand Up @@ -416,6 +421,7 @@ def build_workflow(opts, retval):
debug=opts.debug,
low_mem=opts.low_mem,
anat_only=opts.anat_only,
func_only=opts.func_only,
longitudinal=opts.longitudinal,
omp_nthreads=omp_nthreads,
skull_strip_template=opts.skull_strip_template,
Expand Down
17 changes: 10 additions & 7 deletions fmriprep/interfaces/bids.py
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Expand Up @@ -6,7 +6,7 @@
# @Author: oesteban
# @Date: 2016-06-03 09:35:13
# @Last Modified by: oesteban
# @Last Modified time: 2017-10-10 15:37:47
# @Last Modified time: 2017-10-31 10:01:08
"""
Interfaces for handling BIDS-like neuroimaging structures
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down Expand Up @@ -130,25 +130,28 @@ class BIDSDataGrabber(SimpleInterface):
"""
input_spec = BIDSDataGrabberInputSpec
output_spec = BIDSDataGrabberOutputSpec
_require_funcs = True
_require_func = True
_require_anat = True

def __init__(self, *args, **kwargs):
anat_only = kwargs.pop('anat_only')
anat_only = kwargs.pop('anat_only', False)
func_only = kwargs.pop('func_only', False)
super(BIDSDataGrabber, self).__init__(*args, **kwargs)
if anat_only is not None:
self._require_funcs = not anat_only

self._require_func = anat_only is not True
self._require_anat = func_only is not True

def _run_interface(self, runtime):
bids_dict = self.inputs.subject_data

self._results['out_dict'] = bids_dict
self._results.update(bids_dict)

if not bids_dict['t1w']:
if self._require_anat and not bids_dict['t1w']:
raise FileNotFoundError('No T1w images found for subject sub-{}'.format(
self.inputs.subject_id))

if self._require_funcs and not bids_dict['bold']:
if self._require_func and not bids_dict['bold']:
raise FileNotFoundError('No functional images found for subject sub-{}'.format(
self.inputs.subject_id))

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194 changes: 120 additions & 74 deletions fmriprep/workflows/base.py
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Expand Up @@ -27,11 +27,11 @@
from ..info import __version__

from .anatomical import init_anat_preproc_wf
from .bold import init_func_preproc_wf
from .bold import init_func_preproc_wf, init_onlyfunc_preproc_wf


def init_fmriprep_wf(subject_list, task_id, run_uuid,
ignore, debug, low_mem, anat_only, longitudinal, omp_nthreads,
ignore, debug, low_mem, anat_only, func_only, longitudinal, omp_nthreads,
skull_strip_template, work_dir, output_dir, bids_dir,
freesurfer, output_spaces, template, medial_surface_nan, hires,
use_bbr, bold2t1w_dof, fmap_bspline, fmap_demean, use_syn, force_syn,
Expand All @@ -55,6 +55,7 @@ def init_fmriprep_wf(subject_list, task_id, run_uuid,
debug=False,
low_mem=False,
anat_only=False,
func_only=False,
longitudinal=False,
omp_nthreads=1,
skull_strip_template='OASIS',
Expand Down Expand Up @@ -94,6 +95,8 @@ def init_fmriprep_wf(subject_list, task_id, run_uuid,
Write uncompressed .nii files in some cases to reduce memory usage
anat_only : bool
Disable functional workflows
func_only : bool
Disable anatomical workflows
longitudinal : bool
Treat multiple sessions as longitudinal (may increase runtime)
See sub-workflows for specific differences
Expand Down Expand Up @@ -167,6 +170,7 @@ def init_fmriprep_wf(subject_list, task_id, run_uuid,
debug=debug,
low_mem=low_mem,
anat_only=anat_only,
func_only=func_only,
longitudinal=longitudinal,
omp_nthreads=omp_nthreads,
skull_strip_template=skull_strip_template,
Expand Down Expand Up @@ -203,8 +207,8 @@ def init_fmriprep_wf(subject_list, task_id, run_uuid,


def init_single_subject_wf(subject_id, task_id, name,
ignore, debug, low_mem, anat_only, longitudinal, omp_nthreads,
skull_strip_template, reportlets_dir, output_dir,
ignore, debug, low_mem, anat_only, func_only, longitudinal,
omp_nthreads, skull_strip_template, reportlets_dir, output_dir,
bids_dir, freesurfer, output_spaces, template, medial_surface_nan,
hires, use_bbr, bold2t1w_dof, fmap_bspline, fmap_demean, use_syn,
force_syn, output_grid_ref, use_aroma, ignore_aroma_err):
Expand Down Expand Up @@ -241,6 +245,7 @@ def init_single_subject_wf(subject_id, task_id, name,
debug=False,
low_mem=False,
anat_only=False,
func_only=False,
hires=True,
use_bbr=True,
bold2t1w_dof=9,
Expand Down Expand Up @@ -268,6 +273,8 @@ def init_single_subject_wf(subject_id, task_id, name,
Write uncompressed .nii files in some cases to reduce memory usage
anat_only : bool
Disable functional workflows
func_only : bool
Disable anatomical workflows
longitudinal : bool
Treat multiple sessions as longitudinal (may increase runtime)
See sub-workflows for specific differences
Expand Down Expand Up @@ -342,7 +349,7 @@ def init_single_subject_wf(subject_id, task_id, name,
"All workflows require BOLD images.".format(
subject_id, task_id if task_id else '<all>'))

if not subject_data['t1w']:
if not func_only or not subject_data['t1w']:
raise Exception("No T1w images found for participant {}. "
"All workflows require T1w images.".format(subject_id))

Expand All @@ -351,7 +358,8 @@ def init_single_subject_wf(subject_id, task_id, name,
inputnode = pe.Node(niu.IdentityInterface(fields=['subjects_dir']),
name='inputnode')

bidssrc = pe.Node(BIDSDataGrabber(subject_data=subject_data, anat_only=anat_only),
bidssrc = pe.Node(BIDSDataGrabber(subject_data=subject_data, anat_only=anat_only,
func_only=func_only),
name='bidssrc')

bids_info = pe.Node(BIDSInfo(), name='bids_info', run_without_submitting=True)
Expand All @@ -373,79 +381,117 @@ def init_single_subject_wf(subject_id, task_id, name,
suffix='about'),
name='ds_about_report', run_without_submitting=True)

# Preprocessing of T1w (includes registration to MNI)
anat_preproc_wf = init_anat_preproc_wf(name="anat_preproc_wf",
skull_strip_template=skull_strip_template,
output_spaces=output_spaces,
template=template,
debug=debug,
longitudinal=longitudinal,
omp_nthreads=omp_nthreads,
freesurfer=freesurfer,
hires=hires,
reportlets_dir=reportlets_dir,
output_dir=output_dir,
num_t1w=len(subject_data['t1w']))

workflow.connect([
(inputnode, anat_preproc_wf, [('subjects_dir', 'inputnode.subjects_dir')]),
(bidssrc, bids_info, [(('t1w', fix_multi_T1w_source_name), 'in_file')]),
(inputnode, summary, [('subjects_dir', 'subjects_dir')]),
(bidssrc, summary, [('t1w', 't1w'),
('t2w', 't2w'),
('bold', 'bold')]),
(bids_info, summary, [('subject_id', 'subject_id')]),
(bidssrc, anat_preproc_wf, [('t1w', 'inputnode.t1w'),
('t2w', 'inputnode.t2w')]),
(summary, anat_preproc_wf, [('subject_id', 'inputnode.subject_id')]),
(bidssrc, ds_summary_report, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
(summary, ds_summary_report, [('out_report', 'in_file')]),
(bidssrc, ds_about_report, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
(about, ds_about_report, [('out_report', 'in_file')]),
])

if anat_only:
return workflow

for bold_file in subject_data['bold']:
func_preproc_wf = init_func_preproc_wf(bold_file=bold_file,
layout=layout,
ignore=ignore,
freesurfer=freesurfer,
use_bbr=use_bbr,
bold2t1w_dof=bold2t1w_dof,
reportlets_dir=reportlets_dir,
if not func_only:
# Preprocessing of T1w (includes registration to MNI)
anat_preproc_wf = init_anat_preproc_wf(name="anat_preproc_wf",
skull_strip_template=skull_strip_template,
output_spaces=output_spaces,
template=template,
medial_surface_nan=medial_surface_nan,
output_dir=output_dir,
omp_nthreads=omp_nthreads,
low_mem=low_mem,
fmap_bspline=fmap_bspline,
fmap_demean=fmap_demean,
use_syn=use_syn,
force_syn=force_syn,
debug=debug,
output_grid_ref=output_grid_ref,
use_aroma=use_aroma,
ignore_aroma_err=ignore_aroma_err)
longitudinal=longitudinal,
omp_nthreads=omp_nthreads,
freesurfer=freesurfer,
hires=hires,
reportlets_dir=reportlets_dir,
output_dir=output_dir,
num_t1w=len(subject_data['t1w']))

workflow.connect([
(anat_preproc_wf, func_preproc_wf,
[('outputnode.t1_preproc', 'inputnode.t1_preproc'),
('outputnode.t1_brain', 'inputnode.t1_brain'),
('outputnode.t1_mask', 'inputnode.t1_mask'),
('outputnode.t1_seg', 'inputnode.t1_seg'),
('outputnode.t1_tpms', 'inputnode.t1_tpms'),
('outputnode.t1_2_mni_forward_transform', 'inputnode.t1_2_mni_forward_transform'),
('outputnode.t1_2_mni_reverse_transform', 'inputnode.t1_2_mni_reverse_transform'),
# Undefined if --no-freesurfer, but this is safe
('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id'),
('outputnode.t1_2_fsnative_forward_transform',
'inputnode.t1_2_fsnative_forward_transform'),
('outputnode.t1_2_fsnative_reverse_transform',
'inputnode.t1_2_fsnative_reverse_transform')]),
(inputnode, anat_preproc_wf, [('subjects_dir', 'inputnode.subjects_dir')]),
(bidssrc, bids_info, [(('t1w', fix_multi_T1w_source_name), 'in_file')]),
(inputnode, summary, [('subjects_dir', 'subjects_dir')]),
(bidssrc, summary, [('t1w', 't1w'),
('t2w', 't2w'),
('bold', 'bold')]),
(bids_info, summary, [('subject_id', 'subject_id')]),
(bidssrc, anat_preproc_wf, [('t1w', 'inputnode.t1w'),
('t2w', 'inputnode.t2w')]),
(summary, anat_preproc_wf, [('subject_id', 'inputnode.subject_id')]),
(bidssrc, ds_summary_report, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
(summary, ds_summary_report, [('out_report', 'in_file')]),
(bidssrc, ds_about_report, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
(about, ds_about_report, [('out_report', 'in_file')]),
])

if anat_only:
return workflow

for bold_file in subject_data['bold']:
if not func_only: # Connect anatomical only if possible
func_preproc_wf = init_func_preproc_wf(
bold_file=bold_file,
layout=layout,
ignore=ignore,
freesurfer=freesurfer,
use_bbr=use_bbr,
bold2t1w_dof=bold2t1w_dof,
reportlets_dir=reportlets_dir,
output_spaces=output_spaces,
template=template,
medial_surface_nan=medial_surface_nan,
output_dir=output_dir,
omp_nthreads=omp_nthreads,
low_mem=low_mem,
fmap_bspline=fmap_bspline,
fmap_demean=fmap_demean,
use_syn=use_syn,
force_syn=force_syn,
debug=debug,
output_grid_ref=output_grid_ref,
use_aroma=use_aroma,
ignore_aroma_err=ignore_aroma_err,
)
workflow.connect([
(anat_preproc_wf, func_preproc_wf,
[('outputnode.t1_preproc', 'inputnode.t1_preproc'),
('outputnode.t1_brain', 'inputnode.t1_brain'),
('outputnode.t1_mask', 'inputnode.t1_mask'),
('outputnode.t1_seg', 'inputnode.t1_seg'),
('outputnode.t1_tpms', 'inputnode.t1_tpms'),
('outputnode.t1_2_mni_forward_transform',
'inputnode.t1_2_mni_forward_transform'),
('outputnode.t1_2_mni_reverse_transform',
'inputnode.t1_2_mni_reverse_transform'),
# Undefined if --no-freesurfer, but this is safe
('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id'),
('outputnode.t1_2_fsnative_forward_transform',
'inputnode.t1_2_fsnative_forward_transform'),
('outputnode.t1_2_fsnative_reverse_transform',
'inputnode.t1_2_fsnative_reverse_transform')]),
])

else:
func_preproc_wf = init_onlyfunc_preproc_wf(
bold_file=bold_file,
layout=layout,
ignore=ignore,
reportlets_dir=reportlets_dir,
output_dir=output_dir,
omp_nthreads=omp_nthreads,
low_mem=low_mem,
fmap_bspline=fmap_bspline,
fmap_demean=fmap_demean,
debug=debug,
use_aroma=use_aroma,
ignore_aroma_err=ignore_aroma_err,
)

workflow.connect([
(inputnode, func_preproc_wf, [('subjects_dir', 'inputnode.subjects_dir')]),
(bidssrc, bids_info, [
(('bold', fix_multi_bold_source_name), 'in_file')]),
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fix_multi_bold_source_name is undefined

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I assumed there was an analog to fic_multi_t1w_source_name, which pops up in the anat_only workflow.

(inputnode, summary, [('subjects_dir', 'subjects_dir')]),
(bidssrc, summary, [('bold', 'bold')]),
(bids_info, summary, [('subject_id', 'subject_id')]),
(bidssrc, func_preproc_wf, [('bold', 'inputnode.bold')]),
(summary, func_preproc_wf, [('subject_id', 'inputnode.subject_id')]),
(bidssrc, ds_summary_report, [
(('bold', fix_multi_bold_source_name), 'source_file')]),
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fix_multi_bold_source_name is undefined

(summary, ds_summary_report, [('out_report', 'in_file')]),
(bidssrc, ds_about_report, [
(('bold', fix_multi_bold_source_name), 'source_file')]),
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fix_multi_bold_source_name is undefined

(about, ds_about_report, [('out_report', 'in_file')]),
])

return workflow
2 changes: 1 addition & 1 deletion fmriprep/workflows/bold/__init__.py
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Expand Up @@ -18,7 +18,7 @@

"""

from .base import init_func_preproc_wf
from .base import init_func_preproc_wf, init_onlyfunc_preproc_wf
from .util import init_bold_reference_wf
from .hmc import init_bold_hmc_wf
from .stc import init_bold_stc_wf
Expand Down