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[WIP] ENH: Apply 9 DOF alignment in T1 merge #473

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[WIP] ENH: Apply 9 DOF alignment in T1 merge #473

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cb283eb
RF: Use merged/reoriented T1 as FreeSurfer input
effigies Apr 18, 2017
1cd285e
ENH: Use 9-dof motion correction in T1 merge
effigies Apr 24, 2017
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2 changes: 1 addition & 1 deletion fmriprep/interfaces/images.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ def _run_interface(self, runtime):
magmrg = fsl.Merge(dimension='t', in_files=self.inputs.in_files)
in_files = magmrg.run().outputs.merged_file
mcflirt = fsl.MCFLIRT(cost='normcorr', save_mats=True, save_plots=True,
ref_vol=0, in_file=in_files)
ref_vol=0, dof=9, in_file=in_files)
mcres = mcflirt.run()
self._results['out_mats'] = mcres.outputs.mat_file
self._results['out_movpar'] = mcres.outputs.par_file
Expand Down
21 changes: 7 additions & 14 deletions fmriprep/workflows/anatomical.py
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Expand Up @@ -160,10 +160,9 @@ def init_anat_preproc_wf(skull_strip_ants, debug, freesurfer, ants_nthreads,
if freesurfer:
workflow.connect([
(inputnode, surface_recon_wf, [
('t1w', 'inputnode.t1w'),
('t2w', 'inputnode.t2w'),
('subjects_dir', 'inputnode.subjects_dir')]),
(arw, surface_recon_wf, [('out', 'inputnode.reoriented_t1')]),
(arw, surface_recon_wf, [('out', 'inputnode.t1w')]),
(skullstrip_wf, surface_recon_wf, [
('outputnode.out_file', 'inputnode.skullstripped_t1')]),
(surface_recon_wf, outputnode, [
Expand Down Expand Up @@ -285,7 +284,7 @@ def init_surface_recon_wf(nthreads, hires, reportlets_dir, output_dir,

inputnode = pe.Node(
niu.IdentityInterface(
fields=['t1w', 't2w', 'reoriented_t1', 'skullstripped_t1', 'subjects_dir']),
fields=['t1w', 't2w', 'skullstripped_t1', 'subjects_dir']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['subjects_dir', 'subject_id', 'fs_2_t1_transform']), name='outputnode')
Expand All @@ -301,25 +300,19 @@ def detect_inputs(t1w_list, t2w_list=[], hires_enabled=True):
# Use high resolution preprocessing if voxel size < 1.0mm
# Tolerance of 0.05mm requires that rounds down to 0.9mm or lower
hires = hires_enabled and max(t1w_ref.header.get_zooms()) < 1 - 0.05
t1w_outs = [t1w_list.pop(0)]
for t1w in t1w_list:
img = nib.load(t1w)
if all((img.shape == t1w_ref.shape,
img.header.get_zooms() == t1w_ref.header.get_zooms())):
t1w_outs.append(t1w)

t2w = Undefined
if t2w_list and max(nib.load(t2w_list[0]).header.get_zooms()) < 1.2:
t2w = t2w_list[0]

# https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon
mris_inflate = '-n 50' if hires else Undefined
return (t1w_outs, t2w, isdefined(t2w), hires, mris_inflate)
return (t2w, isdefined(t2w), hires, mris_inflate)

recon_config = pe.Node(
niu.Function(
function=detect_inputs,
output_names=['t1w', 't2w', 'use_T2', 'hires', 'mris_inflate']),
output_names=['t2w', 'use_T2', 'hires', 'mris_inflate']),
name='recon_config',
run_without_submitting=True)
recon_config.inputs.hires_enabled = hires
Expand Down Expand Up @@ -495,8 +488,8 @@ def normalize_surfs(in_file):
(reconall, outputnode, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
# Reconstruction phases
(recon_config, autorecon1, [('t1w', 'T1_files'),
('t2w', 'T2_file'),
(inputnode, autorecon1, [('t1w', 'T1_files')]),
(recon_config, autorecon1, [('t2w', 'T2_file'),
('hires', 'hires'),
# First run only (recon-all saves expert options)
('mris_inflate', 'mris_inflate')]),
Expand All @@ -508,7 +501,7 @@ def normalize_surfs(in_file):
(reconall, recon_report, [('out_report', 'in_file')]),
# Construct transform from FreeSurfer conformed image to FMRIPREP
# reoriented image
(inputnode, fs_transform, [('reoriented_t1', 'target_image')]),
(inputnode, fs_transform, [('t1w', 'target_image')]),
(autorecon1, fs_transform, [('T1', 'moving_image')]),
(fs_transform, outputnode, [('fsl_file', 'fs_2_t1_transform')]),
# Generate midthickness surfaces and save to FreeSurfer derivatives
Expand Down