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Resample surfaces to any space/density using Connectome Workbench. #473

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80c68cf
Resample surfaces to any space/density using Connectome Workbench.
feilong May 1, 2025
ce5f7e8
Remove the print statement, which was for debugging.
feilong May 1, 2025
72e7f8d
Make init_resample_surfaces_wf call init_resample_surfaces_wb_wf to a…
feilong May 1, 2025
be1ab03
rf: Use new resample_surfaces workflow directly
effigies May 22, 2025
e8c0399
feat: Add backwards compatibility and DeprecationWarning
effigies May 22, 2025
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3 changes: 2 additions & 1 deletion src/smriprep/workflows/anatomical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -382,7 +382,8 @@ def init_anat_preproc_wf(
hcp_morphometrics_wf = init_hcp_morphometrics_wf(omp_nthreads=omp_nthreads)
resample_surfaces_wf = init_resample_surfaces_wf(
surfaces=['white', 'pial', 'midthickness'],
grayord_density=cifti_output,
space='fsLR',
density='32k' if cifti_output == '91k' else '59k',
)
morph_grayords_wf = init_morph_grayords_wf(
grayord_density=cifti_output, omp_nthreads=omp_nthreads
Expand Down
46 changes: 31 additions & 15 deletions src/smriprep/workflows/surfaces.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
"""

import typing as ty
import warnings

from nipype.interfaces import freesurfer as fs
from nipype.interfaces import io as nio
Expand Down Expand Up @@ -1318,11 +1319,13 @@ def init_anat_ribbon_wf(name='anat_ribbon_wf'):

def init_resample_surfaces_wf(
surfaces: list[str],
grayord_density: ty.Literal['91k', '170k'],
density: str | None = None,
grayord_density: str | None = None,
space: str = 'fsLR',
name: str = 'resample_surfaces_wf',
):
"""
Resample subject surfaces surface to specified density.
Resample subject surfaces surface to specified space and density.

Workflow Graph
.. workflow::
Expand All @@ -1332,44 +1335,57 @@ def init_resample_surfaces_wf(
from smriprep.workflows.surfaces import init_resample_surfaces_wf
wf = init_resample_surfaces_wf(
surfaces=['white', 'pial', 'midthickness'],
grayord_density='91k',
space='onavg',
density='10k',
)

Parameters
----------
surfaces : :class:`list` of :class:`str`
Names of surfaces (e.g., ``'white'``) to resample. Both hemispheres will be resampled.
grayord_density : :class:`str`
Either `91k` or `170k`, representing the total of vertices or *grayordinates*.
space : :class:`str`
The space to resample to, e.g., ``'onavg'``, ``'fsLR'``.
density : :class:`str`
The density to resample to, e.g., ``'10k'``, ``'41k'``. Number of vertices per hemisphere.
name : :class:`str`
Unique name for the subworkflow (default: ``"resample_surfaces_wf"``)

Inputs
------
``<surface>``
Left and right GIFTIs for each surface name passed to ``surfaces``
Left and right GIFTIs for each surface name passed to ``surfaces``.
sphere_reg_fsLR
GIFTI surface mesh corresponding to the subject's fsLR registration sphere
GIFTI surface mesh corresponding to the subject's fsLR registration sphere.
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Suggested change
GIFTI surface mesh corresponding to the subject's fsLR registration sphere.
GIFTI surface mesh corresponding to the subject's ``space`` registration sphere.


Outputs
-------
``<surface>``
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Suggested change
``<surface>``
``<surface>_<space>``

Left and right GIFTI surface mesh corresponding to the input surface, resampled to fsLR
Left and right GIFTI surface mesh corresponding to the input surface, resampled to the
specified space and density.
"""
import templateflow.api as tf
from niworkflows.engine.workflows import LiterateWorkflow as Workflow

workflow = Workflow(name=name)
if density is None:
if grayord_density is None:
raise ValueError('No density specified. Set density argument.')
density = '32k' if grayord_density == '91k' else '59k'
warnings.warn(
'Deprecated grayord_density passed. Replace with\n\t'
"density='32k' if grayord_density == '91k' else '59k'",
DeprecationWarning,
stacklevel=2,
)

fslr_density = '32k' if grayord_density == '91k' else '59k'
workflow = Workflow(name=name)

inputnode = pe.Node(
niu.IdentityInterface(fields=[*surfaces, 'sphere_reg_fsLR']),
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if the goal is to make this generalizable, this should be sphere_reg_{space}

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I believe that what @feilong has is registrations from fsLR to onavg.

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Yes, by default the sphere.reg generated by MSM is always registered to fsLR.

name='inputnode',
)

outputnode = pe.Node(
niu.IdentityInterface(fields=[f'{surf}_fsLR' for surf in surfaces]), name='outputnode'
niu.IdentityInterface(fields=[f'{surf}_{space}' for surf in surfaces]), name='outputnode'
)

surface_list = pe.Node(
Expand All @@ -1386,11 +1402,11 @@ def init_resample_surfaces_wf(
resampler.inputs.new_sphere = [
str(
tf.get(
template='fsLR',
density=fslr_density,
template=space,
density=density,
suffix='sphere',
hemi=hemi,
space=None,
space=(None if space == 'fsLR' else 'fsLR'),
extension='.surf.gii',
)
)
Comment on lines 1402 to 1412
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altering space in this templateflow query feels brittle - for instance, it will not be able to handle:

https://github.com/nipreps/nibabies/blob/1e6afd415ec2776a4bf749628fa1a58646d536db/nibabies/workflows/anatomical/surfaces.py#L502-L512

thinking we can either extract this out, or add a parameter tf_space to handle this - don't particularly love either tbh

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@feilong feilong May 22, 2025 •
edited
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The usage of space- here resembles tpl-dhcpAsym_cohort-42_space-fsaverage_hemi-L_den-41k_desc-reg_sphere.surf.gii.
It is supposed to get the sphere file that bridges two spaces (e.g., dhcpAsym and fsaverage, onavg and fsLR).

I'm not familiar with dhcpAsym templates. Do the templates also imply space-fsLR when space is not specified?

I prefer to use atlas to refer to the registration target, because the registration target is mainly about the cortical folding patterns, but atlas is also an overloaded term...

Expand All @@ -1416,7 +1432,7 @@ def init_resample_surfaces_wf(
(surface_list, resampler, [('out', 'surface_in')]),
(resampler, surface_groups, [('surface_out', 'inlist')]),
(surface_groups, outputnode, [
(f'out{i}', f'{surf}_fsLR') for i, surf in enumerate(surfaces, start=1)
(f'out{i}', f'{surf}_{space}') for i, surf in enumerate(surfaces, start=1)
]),
]) # fmt:skip

Expand Down
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