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FIX: Correctly detect completed ReconAll steps #1824

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Merged
merged 5 commits into from
Feb 21, 2017
Merged

FIX: Correctly detect completed ReconAll steps #1824

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4a7e6f6
BF: Update ctab file locations to under label/
effigies Feb 17, 2017
d422183
Missing/mislocated v5.3.0 recon-all steps
effigies Feb 17, 2017
9b3e656
Add undocumented v5.3 steps
effigies Feb 17, 2017
03b512c
Do not run recon-all if all steps complete
effigies Feb 17, 2017
cc5d9c9
Fix typo in FSv6 steps
effigies Feb 17, 2017
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47 changes: 37 additions & 10 deletions nipype/interfaces/freesurfer/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -665,6 +665,7 @@ class ReconAll(CommandLine):
input_spec = ReconAllInputSpec
output_spec = ReconAllOutputSpec
_can_resume = True
force_run = False

# Steps are based off of the recon-all tables [0,1] describing, inputs,
# commands, and outputs of each step of the recon-all process,
Expand All @@ -687,7 +688,7 @@ class ReconAll(CommandLine):
], []),
('nuintensitycor', ['mri/nu.mgz'], []),
('normalization', ['mri/T1.mgz'], []),
('skullstrip', ['mri/talairach_with_skull.lta',
('skullstrip', ['mri/transforms/talairach_with_skull.lta',
'mri/brainmask.auto.mgz',
'mri/brainmask.mgz'], []),
]
Expand Down Expand Up @@ -730,6 +731,8 @@ class ReconAll(CommandLine):
'surf/lh.sulc', 'surf/rh.sulc',
'surf/lh.inflated.H', 'surf/rh.inflated.H',
'surf/lh.inflated.K', 'surf/rh.inflated.K'], []),
# Undocumented in ReconAllTableStableV5.3
('curvstats', ['stats/lh.curv.stats', 'stats/rh.curv.stats'], []),
]
_autorecon3_steps = [
('sphere', ['surf/lh.sphere', 'surf/rh.sphere'], []),
Expand All @@ -742,18 +745,29 @@ class ReconAll(CommandLine):
'surf/lh.curv.pial', 'surf/rh.curv.pial',
'surf/lh.area.pial', 'surf/rh.area.pial',
'surf/lh.thickness', 'surf/rh.thickness'], []),
# Misnamed outputs in ReconAllTableStableV5.3: ?h.w-c.pct.mgz
('pctsurfcon', ['surf/lh.w-g.pct.mgh', 'surf/rh.w-g.pct.mgh'], []),
('parcstats', ['stats/lh.aparc.stats', 'stats/rh.aparc.stats',
'label/aparc.annot.a2009s.ctab'], []),
('cortparc2', ['label/lh.aparc.a2009s.annot',
'label/rh.aparc.a2009s.annot'], []),
('parcstats2', ['stats/lh.aparc.a2009s.stats',
'stats/rh.aparc.a2009s.stats',
'stats/aparc.annot.a2009s.ctab'], []),
'label/aparc.annot.a2009s.ctab'], []),
# Undocumented in ReconAllTableStableV5.3
('cortparc3', ['label/lh.aparc.DKTatlas40.annot',
'label/rh.aparc.DKTatlas40.annot'], []),
# Undocumented in ReconAllTableStableV5.3
('parcstats3', ['stats/lh.aparc.a2009s.stats',
'stats/rh.aparc.a2009s.stats',
'label/aparc.annot.a2009s.ctab'], []),
('cortribbon', ['mri/lh.ribbon.mgz', 'mri/rh.ribbon.mgz',
'mri/ribbon.mgz'], []),
('segstats', ['stats/aseg.stats'], []),
('aparc2aseg', ['mri/aparc+aseg.mgz',
'mri/aparc.a2009s+aseg.mgz'], []),
('wmparc', ['mri/wmparc.mgz', 'stats/wmparc.stats'], []),
('balabels', ['BA.ctab', 'BA.thresh.ctab'], []),
('balabels', ['label/BA.ctab', 'label/BA.thresh.ctab'], []),
('label-exvivo-ec', ['label/lh.entorhinal_exvivo.label',
'label/rh.entorhinal_exvivo.label'], []),
]
Expand Down Expand Up @@ -807,18 +821,18 @@ class ReconAll(CommandLine):
'surf/lh.thickness', 'surf/rh.thickness'], []),
('cortribbon', ['mri/lh.ribbon.mgz', 'mri/rh.ribbon.mgz',
'mri/ribbon.mgz'], []),
('parcstats', ['stats/lh.aparc.astats', 'stats/rh.aparc.stats',
'stats/aparc.annot.ctab'], []),
('parcstats', ['stats/lh.aparc.stats', 'stats/rh.aparc.stats',
'label/aparc.annot.ctab'], []),
('cortparc2', ['label/lh.aparc.a2009s.annot',
'label/rh.aparc.a2009s.annot'], []),
('parcstats2', ['stats/lh.aparc.a2009s.stats',
'stats/rh.aparc.a2009s.stats',
'stats/aparc.annot.a2009s.ctab'], []),
'label/aparc.annot.a2009s.ctab'], []),
('cortparc3', ['label/lh.aparc.DKTatlas.annot',
'label/rh.aparc.DKTatlas.annot'], []),
('parcstats3', ['stats/lh.aparc.DKTatlas.stats',
'stats/rh.aparc.DKTatlas.stats',
'stats/aparc.annot.DKTatlas.ctab'], []),
'label/aparc.annot.DKTatlas.ctab'], []),
('pctsurfcon', ['surf/lh.w-g.pct.mgh', 'surf/rh.w-g.pct.mgh'], []),
('hyporelabel', ['mri/aseg.presurf.hypos.mgz'], []),
('aparc2aseg', ['mri/aparc+aseg.mgz',
Expand All @@ -827,7 +841,10 @@ class ReconAll(CommandLine):
('apas2aseg', ['mri/aseg.mgz'], ['mri/aparc+aseg.mgz']),
('segstats', ['stats/aseg.stats'], []),
('wmparc', ['mri/wmparc.mgz', 'stats/wmparc.stats'], []),
('balabels', ['BA.ctab', 'BA.thresh.ctab',
# Note that this is a very incomplete list; however the ctab
# files are last to be touched, so this should be reasonable
('balabels', ['label/BA_exvivo.ctab',
'label/BA_exvivo.thresh.ctab',
'label/lh.entorhinal_exvivo.label',
'label/rh.entorhinal_exvivo.label'], []),
]
Expand Down Expand Up @@ -889,20 +906,30 @@ def cmdline(self):
if not isdefined(subjects_dir):
subjects_dir = self._gen_subjects_dir()

no_run = True
flags = []
for idx, step in enumerate(self._steps):
step, outfiles, infiles = step
flag = '-{}'.format(step)
noflag = '-no{}'.format(step)
if flag in cmd or noflag in cmd:
if noflag in cmd:
continue
elif flag in cmd:
no_run = False
continue

subj_dir = os.path.join(subjects_dir, self.inputs.subject_id)
if check_depends([os.path.join(subj_dir, f) for f in outfiles],
[os.path.join(subj_dir, f) for f in infiles]):
flags.append(noflag)
cmd += ' ' + ' '.join(flags)
else:
no_run = False

if no_run and not self.force_run:
iflogger.info('recon-all complete : Not running')
return "echo recon-all: nothing to do"

cmd += ' ' + ' '.join(flags)
iflogger.info('resume recon-all : %s' % cmd)
return cmd

Expand Down