def init_bold_grayords_wf(grayord_density,
mem_gb,
repetition_time,
name="bold_grayords_wf"):
"""
Sample Grayordinates files onto the fsLR atlas.
Outputs are in CIFTI2 format.
Workflow Graph
.. workflow::
:graph2use: colored
:simple_form: yes
from fprodents.workflows.bold.resampling import init_bold_grayords_wf
wf = init_bold_grayords_wf(mem_gb=0.1, grayord_density='91k')
Parameters
----------
grayord_density : :obj:`str`
Either `91k` or `170k`, representing the total of vertices or *grayordinates*.
mem_gb : :obj:`float`
Size of BOLD file in GB
name : :obj:`str`
Unique name for the subworkflow (default: ``'bold_grayords_wf'``)
Inputs
------
bold_std : :obj:`str`
List of BOLD conversions to standard spaces.
spatial_reference :obj:`str`
List of unique identifiers corresponding to the BOLD standard-conversions.
subjects_dir : :obj:`str`
FreeSurfer's subjects directory.
surf_files : :obj:`str`
List of BOLD files resampled on the fsaverage (ico7) surfaces.
surf_refs :
List of unique identifiers corresponding to the BOLD surface-conversions.
Outputs
-------
cifti_bold : :obj:`str`
List of BOLD grayordinates files - (L)eft and (R)ight.
cifti_variant : :obj:`str`
Only ``'HCP Grayordinates'`` is currently supported.
cifti_metadata : :obj:`str`
Path of metadata files corresponding to ``cifti_bold``.
cifti_density : :obj:`str`
Density (i.e., either `91k` or `170k`) of ``cifti_bold``.
"""
import templateflow.api as tf
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.interfaces.cifti import GenerateCifti
from niworkflows.interfaces.utility import KeySelect
workflow = Workflow(name=name)
workflow.__desc__ = """\
*Grayordinates* files [@hcppipelines] containing {density} samples were also
generated using the highest-resolution ``fsaverage`` as intermediate standardized
surface space.
""".format(density=grayord_density)
fslr_density, mni_density = (("32k", "2") if grayord_density == "91k" else
("59k", "1"))
inputnode = pe.Node(
niu.IdentityInterface(fields=[
"bold_std",
"spatial_reference",
"subjects_dir",
"surf_files",
"surf_refs",
]),
name="inputnode",
)
outputnode = pe.Node(
niu.IdentityInterface(fields=[
"cifti_bold", "cifti_variant", "cifti_metadata", "cifti_density"
]),
name="outputnode",
)
# extract out to BOLD base
select_std = pe.Node(
KeySelect(fields=["bold_std"]),
name="select_std",
run_without_submitting=True,
nohash=True,
)
select_std.inputs.key = "MNI152NLin6Asym_res-%s" % mni_density
select_fs_surf = pe.Node(
KeySelect(fields=["surf_files"]),
name="select_fs_surf",
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB,
)
select_fs_surf.inputs.key = "fsaverage"
# Setup Workbench command. LR ordering for hemi can be assumed, as it is imposed
# by the iterfield of the MapNode in the surface sampling workflow above.
resample = pe.MapNode(
wb.MetricResample(method="ADAP_BARY_AREA", area_metrics=True),
name="resample",
iterfield=[
"in_file",
"out_file",
"new_sphere",
"new_area",
"current_sphere",
"current_area",
],
)
resample.inputs.current_sphere = [
str(
tf.get("fsaverage",
hemi=hemi,
density="164k",
desc="std",
suffix="sphere")) for hemi in "LR"
]
resample.inputs.current_area = [
str(
tf.get(
"fsaverage",
hemi=hemi,
density="164k",
desc="vaavg",
suffix="midthickness",
)) for hemi in "LR"
]
resample.inputs.new_sphere = [
str(
tf.get(
"fsLR",
space="fsaverage",
hemi=hemi,
density=fslr_density,
suffix="sphere",
)) for hemi in "LR"
]
resample.inputs.new_area = [
str(
tf.get(
"fsLR",
hemi=hemi,
density=fslr_density,
desc="vaavg",
suffix="midthickness",
)) for hemi in "LR"
]
resample.inputs.out_file = [
"space-fsLR_hemi-%s_den-%s_bold.gii" % (h, grayord_density)
for h in "LR"
]
gen_cifti = pe.Node(
GenerateCifti(
volume_target="MNI152NLin6Asym",
surface_target="fsLR",
TR=repetition_time,
surface_density=fslr_density,
),
name="gen_cifti",
)
# fmt:off
workflow.connect([
(inputnode, gen_cifti, [('subjects_dir', 'subjects_dir')]),
(inputnode, select_std, [('bold_std', 'bold_std'),
('spatial_reference', 'keys')]),
(inputnode, select_fs_surf, [('surf_files', 'surf_files'),
('surf_refs', 'keys')]),
(select_fs_surf, resample, [('surf_files', 'in_file')]),
(select_std, gen_cifti, [('bold_std', 'bold_file')]),
(resample, gen_cifti, [('out_file', 'surface_bolds')]),
(gen_cifti, outputnode, [('out_file', 'cifti_bold'),
('variant', 'cifti_variant'),
('out_metadata', 'cifti_metadata'),
('density', 'cifti_density')]),
])
# fmt:on
return workflow
def init_asl_grayords_wf(grayord_density,
mem_gb,
repetition_time,
name='asl_grayords_wf'):
"""
Sample Grayordinates files onto the fsLR atlas.
Outputs are in CIFTI2 format.
Workflow Graph
.. workflow::
:graph2use: colored
:simple_form: yes
from aslprep.workflows.asl import init_asl_grayords_wf
wf = init_asl_grayords_wf(mem_gb=0.1, grayord_density='91k')
Parameters
----------
grayord_density : :obj:`str`
Either `91k` or `170k`, representing the total of vertices or *grayordinates*.
mem_gb : :obj:`float`
Size of asl file in GB
name : :obj:`str`
Unique name for the subworkflow (default: ``'asl_grayords_wf'``)
Inputs
------
asl_std : :obj:`str`
List of asl conversions to standard spaces.
spatial_reference :obj:`str`
List of unique identifiers corresponding to the asl standard-conversions.
subjects_dir : :obj:`str`
FreeSurfer's subjects directory.
surf_files : :obj:`str`
List of asl files resampled on the fsaverage (ico7) surfaces.
surf_refs :
List of unique identifiers corresponding to the asl surface-conversions.
Outputs
-------
cifti_asl : :obj:`str`
List of asl grayordinates files - (L)eft and (R)ight.
cifti_variant : :obj:`str`
Only ``'HCP Grayordinates'`` is currently supported.
cifti_metadata : :obj:`str`
Path of metadata files corresponding to ``cifti_asl``.
cifti_density : :obj:`str`
Density (i.e., either `91k` or `170k`) of ``cifti_asl``.
"""
import templateflow.api as tf
from ...niworkflows.engine.workflows import LiterateWorkflow as Workflow
from ...niworkflows.interfaces.cifti import GenerateCifti
from ...niworkflows.interfaces.utility import KeySelect
workflow = Workflow(name=name)
workflow.__desc__ = """\
*Grayordinates* files [@hcppipelines] containing {density} samples were also
generated using the highest-resolution ``fsaverage`` as intermediate standardized
surface space.
""".format(density=grayord_density)
fslr_density, mni_density = ('32k',
'2') if grayord_density == '91k' else ('59k',
'1')
inputnode = pe.Node(niu.IdentityInterface(fields=[
'asl_std',
'spatial_reference',
'subjects_dir',
'surf_files',
'surf_refs',
]),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=[
'cifti_asl',
'cifti_variant',
'cifti_metadata',
'cifti_density',
]),
name='outputnode')
# extract out to asl base
select_std = pe.Node(KeySelect(fields=['asl_std']),
name='select_std',
run_without_submitting=True,
nohash=True)
select_std.inputs.key = 'MNI152NLin6Asym_res-%s' % mni_density
select_fs_surf = pe.Node(KeySelect(fields=['surf_files']),
name='select_fs_surf',
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB)
select_fs_surf.inputs.key = 'fsaverage'
# Setup Workbench command. LR ordering for hemi can be assumed, as it is imposed
# by the iterfield of the MapNode in the surface sampling workflow above.
resample = pe.MapNode(wb.MetricResample(method='ADAP_BARY_AREA',
area_metrics=True),
name='resample',
iterfield=[
'in_file', 'out_file', 'new_sphere', 'new_area',
'current_sphere', 'current_area'
])
resample.inputs.current_sphere = [
str(
tf.get('fsaverage',
hemi=hemi,
density='164k',
desc='std',
suffix='sphere')) for hemi in 'LR'
]
resample.inputs.current_area = [
str(
tf.get('fsaverage',
hemi=hemi,
density='164k',
desc='vaavg',
suffix='midthickness')) for hemi in 'LR'
]
resample.inputs.new_sphere = [
str(
tf.get('fsLR',
space='fsaverage',
hemi=hemi,
density=fslr_density,
suffix='sphere')) for hemi in 'LR'
]
resample.inputs.new_area = [
str(
tf.get('fsLR',
hemi=hemi,
density=fslr_density,
desc='vaavg',
suffix='midthickness')) for hemi in 'LR'
]
resample.inputs.out_file = [
'space-fsLR_hemi-%s_den-%s_asl.gii' % (h, grayord_density)
for h in 'LR'
]
gen_cifti = pe.Node(GenerateCifti(
volume_target='MNI152NLin6Asym',
surface_target='fsLR',
TR=repetition_time,
surface_density=fslr_density,
),
name="gen_cifti")
workflow.connect([
(inputnode, gen_cifti, [('subjects_dir', 'subjects_dir')]),
(inputnode, select_std, [('asl_std', 'asl_std'),
('spatial_reference', 'keys')]),
(inputnode, select_fs_surf, [('surf_files', 'surf_files'),
('surf_refs', 'keys')]),
(select_fs_surf, resample, [('surf_files', 'in_file')]),
(select_std, gen_cifti, [('asl_std', 'asl_file')]),
(resample, gen_cifti, [('out_file', 'surface_asls')]),
(gen_cifti, outputnode, [('out_file', 'cifti_asl'),
('variant', 'cifti_variant'),
('out_metadata', 'cifti_metadata'),
('density', 'cifti_density')]),
])
return workflow
def init_bold_surf_wf(mem_gb,
output_spaces,
medial_surface_nan,
fslr_density=None,
name='bold_surf_wf'):
"""
Sample functional images to FreeSurfer surfaces.
For each vertex, the cortical ribbon is sampled at six points (spaced 20% of thickness apart)
and averaged.
Outputs are in GIFTI format.
Workflow Graph
.. workflow::
:graph2use: colored
:simple_form: yes
from fmriprep.workflows.bold import init_bold_surf_wf
wf = init_bold_surf_wf(mem_gb=0.1,
output_spaces=['T1w', 'fsnative',
'template', 'fsaverage5'],
medial_surface_nan=False)
Parameters
----------
output_spaces : list
List of output spaces functional images are to be resampled to
Target spaces beginning with ``fs`` will be selected for resampling,
such as ``fsaverage`` or related template spaces
If the list contains ``fsnative``, images will be resampled to the
individual subject's native surface
If the list contains ``fsLR``, images will be resampled twice;
first to ``fsaverage`` and then to ``fsLR``.
medial_surface_nan : bool
Replace medial wall values with NaNs on functional GIFTI files
fslr_density : str, optional
Density of fsLR surface (32k or 59k)
Inputs
------
source_file
Motion-corrected BOLD series in T1 space
t1w_preproc
Bias-corrected structural template image
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
t1w2fsnative_xfm
LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space
Outputs
-------
surfaces
BOLD series, resampled to FreeSurfer surfaces
"""
# Ensure volumetric spaces do not sneak into this workflow
spaces = [space for space in output_spaces if space.startswith('fs')]
workflow = Workflow(name=name)
if spaces:
workflow.__desc__ = """\
The BOLD time-series, were resampled to surfaces on the following
spaces: {out_spaces}.
""".format(out_spaces=', '.join(['*%s*' % s for s in spaces]))
inputnode = pe.Node(niu.IdentityInterface(fields=[
'source_file', 't1w_preproc', 'subject_id', 'subjects_dir',
't1w2fsnative_xfm'
]),
name='inputnode')
to_fslr = False
if 'fsLR' in output_spaces:
to_fslr = 'fsaverage' in output_spaces and fslr_density
spaces.pop(spaces.index('fsLR'))
outputnode = pe.Node(niu.IdentityInterface(fields=['surfaces']),
name='outputnode')
def select_target(subject_id, space):
"""Get the target subject ID, given a source subject ID and a target space."""
return subject_id if space == 'fsnative' else space
targets = pe.MapNode(niu.Function(function=select_target),
iterfield=['space'],
name='targets',
mem_gb=DEFAULT_MEMORY_MIN_GB)
targets.inputs.space = spaces
# Rename the source file to the output space to simplify naming later
rename_src = pe.MapNode(niu.Rename(format_string='%(subject)s',
keep_ext=True),
iterfield='subject',
name='rename_src',
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB)
rename_src.inputs.subject = spaces
resampling_xfm = pe.Node(LTAConvert(in_lta='identity.nofile',
out_lta=True),
name='resampling_xfm')
set_xfm_source = pe.Node(ConcatenateLTA(out_type='RAS2RAS'),
name='set_xfm_source')
sampler = pe.MapNode(fs.SampleToSurface(sampling_method='average',
sampling_range=(0, 1, 0.2),
sampling_units='frac',
interp_method='trilinear',
cortex_mask=True,
override_reg_subj=True,
out_type='gii'),
iterfield=['source_file', 'target_subject'],
iterables=('hemi', ['lh', 'rh']),
name='sampler',
mem_gb=mem_gb * 3)
if to_fslr:
filter_fsavg = pe.Node(niu.Function(
function=_select_fsaverage_hemi,
output_names=['fsaverage_bold', 'hemi']),
name='filter_fsavg',
mem_gb=DEFAULT_MEMORY_MIN_GB,
run_without_submitting=True)
rename_fslr = pe.Node(niu.Rename(format_string="%(hemi)s.fsLR",
keep_ext=True,
parse_string=r'^(?P<hemi>\w+)'),
name='rename_fslr',
mem_gb=DEFAULT_MEMORY_MIN_GB,
run_without_submitting=True)
fetch_fslr_tpls = pe.Node(niu.Function(function=_fetch_fslr_templates,
output_names=[
'fsaverage_sphere',
'fslr_sphere',
'fsaverage_midthick',
'fslr_midthick'
]),
name='fetch_fslr_tpls',
mem_gb=DEFAULT_MEMORY_MIN_GB,
overwrite=True)
fetch_fslr_tpls.inputs.den = fslr_density
resample_fslr = pe.Node(wb.MetricResample(method='ADAP_BARY_AREA',
area_metrics=True),
name='resample_fslr')
merge_fslr = pe.Node(niu.Merge(2),
name='merge_fslr',
mem_gb=DEFAULT_MEMORY_MIN_GB,
run_without_submitting=True)
def _basename(in_file):
import os
return os.path.basename(in_file)
workflow.connect([
(sampler, filter_fsavg, [('out_file', 'in_files')]),
(filter_fsavg, fetch_fslr_tpls, [('hemi', 'hemi')]),
(filter_fsavg, rename_fslr, [('fsaverage_bold', 'in_file')]),
(rename_fslr, resample_fslr, [('out_file', 'in_file')]),
(rename_fslr, resample_fslr, [(('out_file', _basename), 'out_file')
]),
(fetch_fslr_tpls, resample_fslr,
[('fsaverage_sphere', 'current_sphere'),
('fslr_sphere', 'new_sphere'),
('fsaverage_midthick', 'current_area'),
('fslr_midthick', 'new_area')]),
(sampler, merge_fslr, [('out_file', 'in1')]),
(resample_fslr, merge_fslr, [('out_file', 'in2')]),
])
merger = pe.JoinNode(niu.Merge(1, ravel_inputs=True),
name='merger',
joinsource='sampler',
joinfield=['in1'],
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB)
if medial_surface_nan:
medial_nans = pe.MapNode(MedialNaNs(),
iterfield=['in_file'],
name='medial_nans',
mem_gb=DEFAULT_MEMORY_MIN_GB)
workflow.connect([
(inputnode, medial_nans, [('subjects_dir', 'subjects_dir')]),
(medial_nans, merger, [('out_file', 'in1')]),
])
update_metadata = pe.MapNode(GiftiSetAnatomicalStructure(),
iterfield='in_file',
name='update_metadata',
mem_gb=DEFAULT_MEMORY_MIN_GB)
workflow.connect([
(inputnode, targets, [('subject_id', 'subject_id')]),
(inputnode, rename_src, [('source_file', 'in_file')]),
(inputnode, resampling_xfm, [('source_file', 'source_file'),
('t1w_preproc', 'target_file')]),
(inputnode, set_xfm_source, [('t1w2fsnative_xfm', 'in_lta2')]),
(resampling_xfm, set_xfm_source, [('out_lta', 'in_lta1')]),
(inputnode, sampler, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(set_xfm_source, sampler, [('out_file', 'reg_file')]),
(targets, sampler, [('out', 'target_subject')]),
(rename_src, sampler, [('out_file', 'source_file')]),
(merger, update_metadata, [('out', 'in_file')]),
(update_metadata, outputnode, [('out_file', 'surfaces')]),
])
if to_fslr and medial_surface_nan:
medial_nans.inputs.density = fslr_density
workflow.connect(merge_fslr, 'out', medial_nans, 'in_file')
elif to_fslr:
workflow.connect(merge_fslr, 'out', merger, 'in1')
elif medial_surface_nan:
workflow.connect(sampler, 'out_file', medial_nans, 'in_file')
else:
workflow.connect(sampler, 'out_file', merger, 'in1')
return workflow