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55 changes: 23 additions & 32 deletions fmriprep/workflows/bold/outputs.py
Original file line number Diff line number Diff line change
Expand Up @@ -163,25 +163,33 @@ def init_func_fit_reports_wf(

Inputs
------
std_t1w
T1w image resampled to standard space
std_mask
Mask of skull-stripped template
subject_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
t1w_conform_report
Conformation report
sdc_boldref
BOLD reference before SDC, in BOLD space
coreg_boldref
BOLD reference after SDC, in BOLD space
boldref2anat_xfm
Affine transform from BOLD reference to anatomical space
boldref2fmap_xfm
Affine transform from BOLD reference to fieldmap space
t1w_preproc
The T1w reference map, which is calculated as the average of bias-corrected
and preprocessed T1w images, defining the anatomical space.
t1w_dseg
Segmentation in T1w space
t1w_mask
Brain (binary) mask estimated by brain extraction.
template
Template space and specifications
t1w_dseg
Segmentation in T1w space
fieldmap
Reconstructed fieldmap, in BOLD space
fmap_ref
Fieldmap reference image, in fieldmap space
subject_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
summary_report
HTML snippet summarizing BOLD processing decisions
validation_report
HTML snippet indicating whether affine metadata were overwritten

"""
from nireports.interfaces.reporting.base import (
Expand Down Expand Up @@ -313,18 +321,6 @@ def init_func_fit_reports_wf(
mem_gb=1,
)

fmap_boldref = pe.Node(
ApplyTransforms(
dimension=3,
default_value=0,
float=True,
invert_transform_flags=[True],
interpolation='LanczosWindowedSinc',
),
name='fmap_boldref',
mem_gb=1,
)

# SDC1
sdcreg_report = pe.Node(
FieldmapReportlet(
Expand Down Expand Up @@ -377,17 +373,12 @@ def init_func_fit_reports_wf(
('coreg_boldref', 'reference_image'),
('boldref2fmap_xfm', 'transforms'),
]),
(inputnode, fmap_boldref, [
('fieldmap', 'input_image'),
('coreg_boldref', 'reference_image'),
('boldref2fmap_xfm', 'transforms'),
]),
(inputnode, sdcreg_report, [
('sdc_boldref', 'reference'),
('fieldmap', 'fieldmap'),
('bold_mask', 'mask'),
]),
(fmapref_boldref, sdcreg_report, [('output_image', 'moving')]),
(fmap_boldref, sdcreg_report, [('output_image', 'fieldmap')]),
(sdcreg_report, ds_sdcreg_report, [('out_report', 'in_file')]),
(inputnode, sdc_report, [
('sdc_boldref', 'before'),
Expand Down
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