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Track proximal sources of functional GIFTIs #3263

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merged 5 commits into from
Mar 29, 2024
Merged

Track proximal sources of functional GIFTIs #3263

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b3d45a0
Add Sources to functional GIFTI outputs.
tsalo Mar 28, 2024
8cc0543
Improve source tracking for GIFTIs.
tsalo Mar 28, 2024
7b543c0
Merge remote-tracking branch 'upstream/master' into track-proximal-so…
tsalo Mar 28, 2024
05dde4b
Merge remote-tracking branch 'upstream/master' into track-proximal-so…
tsalo Mar 29, 2024
79eb79e
Drop T1w-space output as a surface Source.
tsalo Mar 29, 2024
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31 changes: 31 additions & 0 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -514,6 +514,37 @@
(bold_anat_wf, bold_surf_wf, [('outputnode.bold_file', 'inputnode.bold_t1w')]),
]) # fmt:skip

if nonstd_spaces.intersection(('anat', 'T1w')):
# Source file should be output T1w-space volumetric file and fsnative2t1w_xfm
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merge_surface_sources = pe.Node(

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niu.Merge(2),
name='merge_surface_sources',
run_without_submitting=True,
)
workflow.connect([

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(ds_bold_t1_wf, merge_surface_sources, [('outputnode.bold', 'in1')]),
(inputnode, merge_surface_sources, [('fsnative2t1w_xfm', 'in2')]),
]) # fmt:skip
else:
# sources are bold_file, motion_xfm, boldref2anat_xfm, fsnative2t1w_xfm
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I would include the white-matter and pial surfaces for each hemisphere, since those determine the coordinates at which the BOLD is sampled. If that's difficult to do at the moment, I'm fine with postponing it to another PR.

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The hemisphere loop happens within init_bold_surf_wf, so I need to add those sources there, but I can't pin down where exactly those two files are grabbed in the workflow. I think it'll have to wait for another PR.

merge_surface_sources = pe.Node(
niu.Merge(4),
name='merge_surface_sources',
run_without_submitting=True,
)
merge_surface_sources.inputs.in1 = bold_file
workflow.connect([
(bold_fit_wf, merge_surface_sources, [
('outputnode.motion_xfm', 'in2'),
('outputnode.boldref2anat_xfm', 'in3'),
]),
(inputnode, merge_surface_sources, [
('fsnative2t1w_xfm', 'in4'),
]),
]) # fmt:skip

workflow.connect([(merge_surface_sources, bold_surf_wf, [('out', 'inputnode.sources')])])

if config.workflow.cifti_output:
from .resampling import (
init_bold_fsLR_resampling_wf,
Expand Down
9 changes: 9 additions & 0 deletions fmriprep/workflows/bold/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -746,6 +746,14 @@ def init_ds_volumes_wf(
),
name='inputnode',
)
outputnode = pe.Node(
niu.IdentityInterface(
fields=[
'bold',
],
),
name='outputnode',
)
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sources = pe.Node(
BIDSURI(
Expand Down Expand Up @@ -791,6 +799,7 @@ def init_ds_volumes_wf(
('resolution', 'resolution'),
]),
(sources, ds_bold, [('out', 'Sources')]),
(ds_bold, outputnode, [('out_file', 'bold')]),
]) # fmt:skip

resample_ref = pe.Node(
Expand Down
30 changes: 22 additions & 8 deletions fmriprep/workflows/bold/resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,9 @@
from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
from niworkflows.interfaces.freesurfer import MedialNaNs

from ... import config
from ...config import DEFAULT_MEMORY_MIN_GB
from ...interfaces.bids import BIDSURI
from ...interfaces.workbench import MetricDilate, MetricMask, MetricResample
from ...utils.bids import dismiss_echo
from .outputs import prepare_timing_parameters
Expand Down Expand Up @@ -93,6 +95,8 @@ def init_bold_surf_wf(
------
source_file
Original BOLD series
sources
List of files used to create the output files.
bold_t1w
Motion-corrected BOLD series in T1 space
subjects_dir
Expand Down Expand Up @@ -128,6 +132,7 @@ def init_bold_surf_wf(
niu.IdentityInterface(
fields=[
'source_file',
'sources',
'bold_t1w',
'subject_id',
'subjects_dir',
Expand All @@ -139,6 +144,15 @@ def init_bold_surf_wf(
itersource = pe.Node(niu.IdentityInterface(fields=['target']), name='itersource')
itersource.iterables = [('target', surface_spaces)]

surfs_sources = pe.Node(
BIDSURI(
numinputs=1,
dataset_links=config.execution.dataset_links,
out_dir=str(config.execution.fmriprep_dir.absolute()),
),
name='surfs_sources',
)

get_fsnative = pe.Node(FreeSurferSource(), name='get_fsnative', run_without_submitting=True)

def select_target(subject_id, space):
Expand Down Expand Up @@ -212,6 +226,8 @@ def select_target(subject_id, space):
(itk2lta, sampler, [('out_inv', 'reg_file')]),
(targets, sampler, [('out', 'target_subject')]),
(inputnode, ds_bold_surfs, [('source_file', 'source_file')]),
(inputnode, surfs_sources, [('sources', 'in1')]),
(surfs_sources, ds_bold_surfs, [('out', 'Sources')]),
(itersource, ds_bold_surfs, [('target', 'space')]),
(update_metadata, ds_bold_surfs, [('out_file', 'in_file')]),
]) # fmt:skip
Expand Down Expand Up @@ -488,14 +504,12 @@ def _calc_lower_thr(in_stats):
)

# apply goodvoxels ribbon mask to bold
workflow.connect(
[
(goodvoxels_mask, goodvoxels_ribbon_mask, [('out_file', 'in_file')]),
(ribbon_boldsrc_xfm, goodvoxels_ribbon_mask, [('output_image', 'mask_file')]),
(goodvoxels_mask, outputnode, [('out_file', 'goodvoxels_mask')]),
(goodvoxels_ribbon_mask, outputnode, [('out_file', 'goodvoxels_ribbon')]),
]
)
workflow.connect([
(goodvoxels_mask, goodvoxels_ribbon_mask, [('out_file', 'in_file')]),
(ribbon_boldsrc_xfm, goodvoxels_ribbon_mask, [('output_image', 'mask_file')]),
(goodvoxels_mask, outputnode, [('out_file', 'goodvoxels_mask')]),
(goodvoxels_ribbon_mask, outputnode, [('out_file', 'goodvoxels_ribbon')]),
]) # fmt:skip

return workflow

Expand Down