def test_generate_report(self):
report_interface = ReconAllRPT(subject_id='fsaverage',
directive='all',
subjects_dir=os.getenv('SUBJECTS_DIR'),
generate_report=True,
out_report='test.svg')
report_interface.mock_run = True
_smoke_test_report(report_interface, 'testReconAll.svg')
def test_ReconAllRPT(monkeypatch):
# Patch the _run_interface method
monkeypatch.setattr(ReconAllRPT, '_run_interface', _run_interface_mock)
rall_rpt = ReconAllRPT(subject_id='fsaverage',
directive='all',
subjects_dir=os.getenv('SUBJECTS_DIR'),
generate_report=True)
_smoke_test_report(rall_rpt, 'testReconAll.svg')
def test_ReconAllRPT(monkeypatch):
# Patch the _run_interface method
monkeypatch.setattr(ReconAllRPT, "_run_interface", _run_interface_mock)
rall_rpt = ReconAllRPT(
subject_id="fsaverage",
directive="all",
subjects_dir=os.getenv("SUBJECTS_DIR"),
generate_report=True,
)
_smoke_test_report(rall_rpt, "testReconAll.svg")
def init_autorecon_resume_wf(omp_nthreads, name='autorecon_resume_wf'):
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(fields=['subjects_dir', 'subject_id', 'use_T2']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['subjects_dir', 'subject_id', 'out_report']),
name='outputnode')
autorecon2_vol = pe.Node(fs.ReconAll(directive='autorecon2-volonly',
openmp=omp_nthreads),
n_procs=omp_nthreads,
name='autorecon2_vol')
autorecon_surfs = pe.MapNode(fs.ReconAll(
directive='autorecon-hemi',
flags=[
'-noparcstats', '-nocortparc2', '-noparcstats2', '-nocortparc3',
'-noparcstats3', '-nopctsurfcon', '-nohyporelabel',
'-noaparc2aseg', '-noapas2aseg', '-nosegstats', '-nowmparc',
'-nobalabels'
],
openmp=omp_nthreads),
iterfield='hemi',
n_procs=omp_nthreads,
name='autorecon_surfs')
autorecon_surfs.inputs.hemi = ['lh', 'rh']
autorecon3 = pe.MapNode(fs.ReconAll(directive='autorecon3',
openmp=omp_nthreads),
iterfield='hemi',
n_procs=omp_nthreads,
name='autorecon3')
autorecon3.inputs.hemi = ['lh', 'rh']
# Only generate the report once; should be nothing to do
recon_report = pe.Node(ReconAllRPT(directive='autorecon3',
generate_report=True),
name='recon_report')
def _dedup(in_list):
vals = set(in_list)
if len(vals) > 1:
raise ValueError(
"Non-identical values can't be deduplicated:\n{!r}".format(
in_list))
return vals.pop()
workflow.connect([
(inputnode, autorecon3, [('use_T2', 'use_T2')]),
(inputnode, autorecon2_vol, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(autorecon2_vol, autorecon_surfs, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(autorecon_surfs, autorecon3,
[(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
(autorecon3, outputnode, [(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
(autorecon3, recon_report, [(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
(recon_report, outputnode, [('out_report', 'out_report')]),
])
return workflow
def init_autorecon_resume_wf(omp_nthreads, name='autorecon_resume_wf'):
r"""
This workflow resumes recon-all execution, assuming the `-autorecon1` stage
has been completed.
In order to utilize resources efficiently, this is broken down into five
sub-stages; after the first stage, the second and third stages may be run
simultaneously, and the fourth and fifth stages may be run simultaneously,
if resources permit::
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon2-volonly
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon-hemi lh \
-noparcstats -nocortparc2 -noparcstats2 -nocortparc3 \
-noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg \
-noapas2aseg -nosegstats -nowmparc -nobalabels
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon-hemi rh \
-noparcstats -nocortparc2 -noparcstats2 -nocortparc3 \
-noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg \
-noapas2aseg -nosegstats -nowmparc -nobalabels
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon3 -hemi lh -T2pial
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon3 -hemi rh -T2pial
The excluded steps in the second and third stages (``-no<option>``) are not
fully hemisphere independent, and are therefore postponed to the final two
stages.
.. workflow::
:graph2use: orig
:simple_form: yes
from smriprep.workflows.surfaces import init_autorecon_resume_wf
wf = init_autorecon_resume_wf(omp_nthreads=1)
**Inputs**
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
use_T2
Refine pial surface using T2w image
use_FLAIR
Refine pial surface using FLAIR image
**Outputs**
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
out_report
Reportlet visualizing quality of surface alignment
"""
workflow = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['subjects_dir', 'subject_id', 'use_T2', 'use_FLAIR']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['subjects_dir', 'subject_id', 'out_report']),
name='outputnode')
autorecon2_vol = pe.Node(fs.ReconAll(directive='autorecon2-volonly',
openmp=omp_nthreads),
n_procs=omp_nthreads,
mem_gb=5,
name='autorecon2_vol')
autorecon2_vol.interface._always_run = True
autorecon_surfs = pe.MapNode(fs.ReconAll(
directive='autorecon-hemi',
flags=[
'-noparcstats', '-nocortparc2', '-noparcstats2', '-nocortparc3',
'-noparcstats3', '-nopctsurfcon', '-nohyporelabel',
'-noaparc2aseg', '-noapas2aseg', '-nosegstats', '-nowmparc',
'-nobalabels'
],
openmp=omp_nthreads),
iterfield='hemi',
n_procs=omp_nthreads,
mem_gb=5,
name='autorecon_surfs')
autorecon_surfs.inputs.hemi = ['lh', 'rh']
autorecon_surfs.interface._always_run = True
autorecon3 = pe.MapNode(fs.ReconAll(directive='autorecon3',
openmp=omp_nthreads),
iterfield='hemi',
n_procs=omp_nthreads,
mem_gb=5,
name='autorecon3')
autorecon3.inputs.hemi = ['lh', 'rh']
autorecon3.interface._always_run = True
# Only generate the report once; should be nothing to do
recon_report = pe.Node(ReconAllRPT(directive='autorecon3',
generate_report=True),
name='recon_report',
mem_gb=5)
recon_report.interface._always_run = True
def _dedup(in_list):
vals = set(in_list)
if len(vals) > 1:
raise ValueError(
"Non-identical values can't be deduplicated:\n{!r}".format(
in_list))
return vals.pop()
workflow.connect([
(inputnode, autorecon3, [('use_T2', 'use_T2'),
('use_FLAIR', 'use_FLAIR')]),
(inputnode, autorecon2_vol, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(autorecon2_vol, autorecon_surfs, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(autorecon_surfs, autorecon3,
[(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
(autorecon3, outputnode, [(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
(autorecon3, recon_report, [(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
(recon_report, outputnode, [('out_report', 'out_report')]),
])
return workflow