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[RTM] FIX: Use t1_2_fsnative registration when sampling to surface #762

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merged 3 commits into from Oct 17, 2017
Merged

[RTM] FIX: Use t1_2_fsnative registration when sampling to surface #762

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e8b016b
FIX: Use t1_2_fsnative registration when sampling to surface
effigies Oct 16, 2017
2217321
ENH: Reset the source affine to BOLD resolution
effigies Oct 16, 2017
05c5efe
DOC: Update docstrings
effigies Oct 16, 2017
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23 changes: 17 additions & 6 deletions fmriprep/workflows/anatomical.py
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Expand Up @@ -156,6 +156,8 @@ def init_anat_preproc_wf(skull_strip_ants, skull_strip_template, output_spaces,
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
t1_2_fsnative_forward_transform
LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space
t1_2_fsnative_reverse_transform
LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w
surfaces
Expand All @@ -177,7 +179,8 @@ def init_anat_preproc_wf(skull_strip_ants, skull_strip_template, output_spaces,
fields=['t1_preproc', 't1_brain', 't1_mask', 't1_seg', 't1_tpms',
't1_2_mni', 't1_2_mni_forward_transform', 't1_2_mni_reverse_transform',
'mni_mask', 'mni_seg', 'mni_tpms',
'subjects_dir', 'subject_id', 't1_2_fsnative_reverse_transform', 'surfaces']),
'subjects_dir', 'subject_id', 't1_2_fsnative_forward_transform',
't1_2_fsnative_reverse_transform', 'surfaces']),
name='outputnode')

# 0. Reorient T1w image(s) to RAS and resample to common voxel space
Expand Down Expand Up @@ -319,6 +322,7 @@ def len_above_thresh(in_list, threshold, longitudinal):
(surface_recon_wf, outputnode, [
('outputnode.subjects_dir', 'subjects_dir'),
('outputnode.subject_id', 'subject_id'),
('outputnode.t1_2_fsnative_forward_transform', 't1_2_fsnative_forward_transform'),
('outputnode.t1_2_fsnative_reverse_transform', 't1_2_fsnative_reverse_transform'),
('outputnode.surfaces', 'surfaces')]),
])
Expand Down Expand Up @@ -368,7 +372,7 @@ def len_above_thresh(in_list, threshold, longitudinal):
('mni_mask', 'inputnode.mni_mask'),
('mni_seg', 'inputnode.mni_seg'),
('mni_tpms', 'inputnode.mni_tpms'),
('t1_2_fsnative_reverse_transform', 'inputnode.t1_2_fsnative_reverse_transform'),
('t1_2_fsnative_forward_transform', 'inputnode.t1_2_fsnative_forward_transform'),
('surfaces', 'inputnode.surfaces'),
]),
])
Expand Down Expand Up @@ -516,6 +520,8 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
t1_2_fsnative_forward_transform
LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space
t1_2_fsnative_reverse_transform
LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w
surfaces
Expand All @@ -538,7 +544,8 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
name='inputnode')
outputnode = pe.Node(
niu.IdentityInterface(
fields=['subjects_dir', 'subject_id', 't1_2_fsnative_reverse_transform', 'surfaces',
fields=['subjects_dir', 'subject_id', 't1_2_fsnative_forward_transform',
't1_2_fsnative_reverse_transform', 'surfaces',
'out_report']),
name='outputnode')

Expand All @@ -559,6 +566,8 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):

fsnative_2_t1_xfm = pe.Node(fs.RobustRegister(auto_sens=True, est_int_scale=True),
name='fsnative_2_t1_xfm')
t1_2_fsnative_xfm = pe.Node(fs.utils.LTAConvert(out_lta=True, invert=True),
name='t1_2_fsnative_xfm')

autorecon_resume_wf = init_autorecon_resume_wf(omp_nthreads=omp_nthreads)
gifti_surface_wf = init_gifti_surface_wf()
Expand Down Expand Up @@ -591,11 +600,13 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
(autorecon1, fsnative_2_t1_xfm, [('T1', 'source_file')]),
(fsnative_2_t1_xfm, gifti_surface_wf, [
('out_reg_file', 'inputnode.t1_2_fsnative_reverse_transform')]),
(fsnative_2_t1_xfm, t1_2_fsnative_xfm, [('out_reg_file', 'in_lta')]),
# Output
(autorecon_resume_wf, outputnode, [('outputnode.subjects_dir', 'subjects_dir'),
('outputnode.subject_id', 'subject_id'),
('outputnode.out_report', 'out_report')]),
(gifti_surface_wf, outputnode, [('outputnode.surfaces', 'surfaces')]),
(t1_2_fsnative_xfm, outputnode, [('out_lta', 't1_2_fsnative_forward_transform')]),
(fsnative_2_t1_xfm, outputnode, [('out_reg_file', 't1_2_fsnative_reverse_transform')]),
])

Expand Down Expand Up @@ -875,7 +886,7 @@ def init_anat_derivatives_wf(output_dir, output_spaces, template, freesurfer,
fields=['source_file', 't1_preproc', 't1_mask', 't1_seg', 't1_tpms',
't1_2_mni_forward_transform', 't1_2_mni_reverse_transform',
't1_2_mni', 'mni_mask', 'mni_seg', 'mni_tpms',
't1_2_fsnative_reverse_transform', 'surfaces']),
't1_2_fsnative_forward_transform', 'surfaces']),
name='inputnode')

ds_t1_preproc = pe.Node(
Expand Down Expand Up @@ -930,7 +941,7 @@ def init_anat_derivatives_wf(output_dir, output_spaces, template, freesurfer,
DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt(template, 'warp')),
name='ds_t1_mni_warp', run_without_submitting=True)

lta_2_itk = pe.Node(fs.utils.LTAConvert(out_itk=True, invert=True), name='lta_2_itk')
lta_2_itk = pe.Node(fs.utils.LTAConvert(out_itk=True), name='lta_2_itk')

ds_t1_fsnative = pe.Node(
DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt('fsnative', 'affine')),
Expand Down Expand Up @@ -959,7 +970,7 @@ def init_anat_derivatives_wf(output_dir, output_spaces, template, freesurfer,

if freesurfer:
workflow.connect([
(inputnode, lta_2_itk, [('t1_2_fsnative_reverse_transform', 'in_lta')]),
(inputnode, lta_2_itk, [('t1_2_fsnative_forward_transform', 'in_lta')]),
(inputnode, ds_t1_fsnative, [('source_file', 'source_file')]),
(lta_2_itk, ds_t1_fsnative, [('out_itk', 'in_file')]),
(inputnode, name_surfs, [('surfaces', 'in_file')]),
Expand Down
18 changes: 8 additions & 10 deletions fmriprep/workflows/base.py
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Expand Up @@ -447,16 +447,14 @@ def init_single_subject_wf(subject_id, task_id, name,
('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')])
])

if freesurfer:
workflow.connect([
(anat_preproc_wf, func_preproc_wf,
[('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id'),
('outputnode.t1_2_fsnative_reverse_transform',
'inputnode.t1_2_fsnative_reverse_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')]),
])

return workflow
37 changes: 28 additions & 9 deletions fmriprep/workflows/bold.py
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Expand Up @@ -179,8 +179,10 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
t1_2_fsnative_forward_transform
LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space
t1_2_fsnative_reverse_transform
Affine transform from FreeSurfer subject space to T1w space
LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w


**Outputs**
Expand Down Expand Up @@ -268,7 +270,8 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
inputnode = pe.Node(niu.IdentityInterface(
fields=['bold_file', 't1_preproc', 't1_brain', 't1_mask', 't1_seg', 't1_tpms',
't1_2_mni_forward_transform', 't1_2_mni_reverse_transform',
'subjects_dir', 'subject_id', 't1_2_fsnative_reverse_transform']),
'subjects_dir', 'subject_id', 't1_2_fsnative_forward_transform',
't1_2_fsnative_reverse_transform']),
name='inputnode')
inputnode.inputs.bold_file = bold_file

Expand Down Expand Up @@ -572,8 +575,11 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
medial_surface_nan=medial_surface_nan,
name='bold_surf_wf')
workflow.connect([
(inputnode, bold_surf_wf, [('subjects_dir', 'inputnode.subjects_dir'),
('subject_id', 'inputnode.subject_id')]),
(inputnode, bold_surf_wf, [
('t1_preproc', 'inputnode.t1_preproc'),
('subjects_dir', 'inputnode.subjects_dir'),
('subject_id', 'inputnode.subject_id'),
('t1_2_fsnative_forward_transform', 'inputnode.t1_2_fsnative_forward_transform')]),
(bold_reg_wf, bold_surf_wf, [('outputnode.bold_t1', 'inputnode.source_file')]),
(bold_surf_wf, outputnode, [('outputnode.surfaces', 'surfaces')]),
])
Expand Down Expand Up @@ -897,7 +903,7 @@ def init_bold_reg_wf(freesurfer, use_bbr, bold2t1w_dof, bold_file_size_gb, omp_n
subject_id
FreeSurfer subject ID
t1_2_fsnative_reverse_transform
Affine transform from FreeSurfer subject space to T1w space
LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w
fieldwarp
a :abbr:`DFM (displacements field map)` in ITK format

Expand Down Expand Up @@ -1041,10 +1047,14 @@ def init_bold_surf_wf(output_spaces, medial_surface_nan, name='bold_surf_wf'):

source_file
Motion-corrected BOLD series in T1 space
t1_preproc
Bias-corrected structural template image
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
t1_2_fsnative_forward_transform
LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space

**Outputs**

Expand All @@ -1054,7 +1064,8 @@ def init_bold_surf_wf(output_spaces, medial_surface_nan, name='bold_surf_wf'):
"""
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(fields=['source_file', 'subject_id', 'subjects_dir']),
niu.IdentityInterface(fields=['source_file', 't1_preproc', 'subject_id', 'subjects_dir',
't1_2_fsnative_forward_transform']),
name='inputnode')

outputnode = pe.Node(niu.IdentityInterface(fields=['surfaces']), name='outputnode')
Expand All @@ -1076,11 +1087,14 @@ def select_target(subject_id, space):
mem_gb=DEFAULT_MEMORY_MIN_GB)
rename_src.inputs.subject = spaces

resampling_xfm = pe.Node(fs.utils.LTAConvert(in_lta='identity.nofile', out_lta=True),
name='resampling_xfm')
set_xfm_source = pe.Node(fs.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', reg_header=True,
interp_method='trilinear', cortex_mask=True,
out_type='gii'),
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')
Expand Down Expand Up @@ -1121,8 +1135,13 @@ def medial_wall_to_nan(in_file, subjects_dir, target_subject):
workflow.connect([
(inputnode, targets, [('subject_id', 'subject_id')]),
(inputnode, rename_src, [('source_file', 'in_file')]),
(inputnode, resampling_xfm, [('source_file', 'source_file'),
('t1_preproc', 'target_file')]),
(inputnode, set_xfm_source, [('t1_2_fsnative_forward_transform', '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')]),
Expand Down