Skip to content

[ENH] Update ReconAll interface for v6 #1790

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 8 commits into from
Feb 8, 2017
Merged

[ENH] Update ReconAll interface for v6 #1790

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
ee9fb50
WIP Update ReconAll interface for v6
effigies Jan 24, 2017
75cae9f
Prevent resume flags from clobbering explicit args
effigies Jan 27, 2017
141267f
Add optional dependencies to ReconAll._steps
effigies Jan 30, 2017
8e914f3
Remove faulty directive overrides
effigies Jan 30, 2017
b8d2b08
Re-add v5.3 steps
effigies Feb 1, 2017
03a7932
Test check_depends
effigies Feb 1, 2017
2752945
Update changelog
effigies Feb 1, 2017
06a9eb9
Add -parallel flag to ReconAll
effigies Feb 7, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGES
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ Upcoming release 0.13
* ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
* ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
(https://github.com/nipy/nipype/pull/1654)
* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)

Release 0.12.1 (August 3, 2016)
===============================
Expand Down
289 changes: 192 additions & 97 deletions nipype/interfaces/freesurfer/preprocess.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,21 +21,29 @@
import numpy as np
from nibabel import load

from ... import logging
from ...utils.filemanip import fname_presuffix
from ... import logging, LooseVersion
from ...utils.filemanip import fname_presuffix, check_depends
from ..io import FreeSurferSource
from ..base import (TraitedSpec, File, traits,
Directory, InputMultiPath,
OutputMultiPath, CommandLine,
CommandLineInputSpec, isdefined)
from .base import (FSCommand, FSTraitedSpec,
FSTraitedSpecOpenMP,
FSCommandOpenMP)
FSCommandOpenMP, Info)
from .utils import copy2subjdir

__docformat__ = 'restructuredtext'
iflogger = logging.getLogger('interface')

FSVersion = "0"
_ver = Info.version()
if _ver:
if 'dev' in _ver:
FSVersion = _ver.rstrip().split('-')[-1] + '.dev'
else:
FSVersion = _ver.rstrip().split('-v')[-1]


class ParseDICOMDirInputSpec(FSTraitedSpec):
dicom_dir = Directory(exists=True, argstr='--d %s', mandatory=True,
Expand Down Expand Up @@ -622,6 +630,8 @@ class ReconAllInputSpec(CommandLineInputSpec):
desc='Use converted T2 to refine the cortical surface')
openmp = traits.Int(argstr="-openmp %d",
desc="Number of processors to use in parallel")
parallel = traits.Bool(argstr="-parallel",
desc="Enable parallel execution")
subjects_dir = Directory(exists=True, argstr='-sd %s', hash_files=False,
desc='path to subjects directory', genfile=True)
flags = traits.Str(argstr='%s', desc='additional parameters')
Expand Down Expand Up @@ -656,85 +666,173 @@ class ReconAll(CommandLine):
output_spec = ReconAllOutputSpec
_can_resume = True

_steps = [
# autorecon1
('motioncor', ['mri/rawavg.mgz', 'mri/orig.mgz']),
('talairach', ['mri/transforms/talairach.auto.xfm',
'mri/transforms/talairach.xfm']),
('nuintensitycor', ['mri/nu.mgz']),
('normalization', ['mri/T1.mgz']),
('skullstrip',
['mri/brainmask.auto.mgz',
'mri/brainmask.mgz']),
# autorecon2
('gcareg', ['mri/transforms/talairach.lta']),
('canorm', ['mri/norm.mgz']),
('careg', ['mri/transforms/talairach.m3z']),
('careginv', ['mri/transforms/talairach.m3z.inv.x.mgz',
'mri/transforms/talairach.m3z.inv.y.mgz',
'mri/transforms/talairach.m3z.inv.z.mgz']),
('rmneck', ['mri/nu_noneck.mgz']),
('skull-lta', ['mri/transforms/talairach_with_skull_2.lta']),
('calabel',
['mri/aseg.auto_noCCseg.mgz', 'mri/aseg.auto.mgz', 'mri/aseg.mgz']),
('normalization2', ['mri/brain.mgz']),
('maskbfs', ['mri/brain.finalsurfs.mgz']),
('segmentation', ['mri/wm.asegedit.mgz', 'mri/wm.mgz']),
('fill', ['mri/filled.mgz']),
('tessellate', ['surf/lh.orig.nofix', 'surf/rh.orig.nofix']),
('smooth1', ['surf/lh.smoothwm.nofix', 'surf/rh.smoothwm.nofix']),
('inflate1', ['surf/lh.inflated.nofix', 'surf/rh.inflated.nofix']),
('qsphere', ['surf/lh.qsphere.nofix', 'surf/rh.qsphere.nofix']),
('fix', ['surf/lh.orig', 'surf/rh.orig']),
('white',
['surf/lh.white',
'surf/rh.white',
'surf/lh.curv',
'surf/rh.curv',
'surf/lh.area',
'surf/rh.area',
'label/lh.cortex.label',
'label/rh.cortex.label']),
('smooth2', ['surf/lh.smoothwm', 'surf/rh.smoothwm']),
('inflate2',
['surf/lh.inflated',
'surf/rh.inflated',
'surf/lh.sulc',
'surf/rh.sulc',
'surf/lh.inflated.H',
'surf/rh.inflated.H',
'surf/lh.inflated.K',
'surf/rh.inflated.K']),
# autorecon3
('sphere', ['surf/lh.sphere', 'surf/rh.sphere']),
('surfreg', ['surf/lh.sphere.reg', 'surf/rh.sphere.reg']),
('jacobian_white', ['surf/lh.jacobian_white',
'surf/rh.jacobian_white']),
('avgcurv', ['surf/lh.avg_curv', 'surf/rh.avg_curv']),
('cortparc', ['label/lh.aparc.annot', 'label/rh.aparc.annot']),
('pial',
['surf/lh.pial',
'surf/rh.pial',
'surf/lh.curv.pial',
'surf/rh.curv.pial',
'surf/lh.area.pial',
'surf/rh.area.pial',
'surf/lh.thickness',
'surf/rh.thickness']),
('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']),
('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']),
('label-exvivo-ec', ['label/lh.entorhinal_exvivo.label',
'label/rh.entorhinal_exvivo.label'])]
# Steps are based off of the recon-all tables [0,1] describing, inputs,
# commands, and outputs of each step of the recon-all process,
# controlled by flags.
#
# Each step is a 3-tuple containing (flag, [outputs], [inputs])
# A step is considered complete if all of its outputs exist and are newer
# than the inputs. An empty input list indicates input mtimes will not
# be checked. This may need updating, if users are working with manually
# edited files.
#
# [0] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3
# [1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0
_autorecon1_steps = [
('motioncor', ['mri/rawavg.mgz', 'mri/orig.mgz'], []),
('talairach', ['mri/orig_nu.mgz',
'mri/transforms/talairach.auto.xfm',
'mri/transforms/talairach.xfm',
# 'mri/transforms/talairach_avi.log',
], []),
('nuintensitycor', ['mri/nu.mgz'], []),
('normalization', ['mri/T1.mgz'], []),
('skullstrip', ['mri/talairach_with_skull.lta',
'mri/brainmask.auto.mgz',
'mri/brainmask.mgz'], []),
]
if LooseVersion(FSVersion) < LooseVersion("6.0.0"):
_autorecon2_steps = [
('gcareg', ['mri/transforms/talairach.lta'], []),
('canorm', ['mri/norm.mgz'], []),
('careg', ['mri/transforms/talairach.m3z'], []),
('careginv', ['mri/transforms/talairach.m3z.inv.x.mgz',
'mri/transforms/talairach.m3z.inv.y.mgz',
'mri/transforms/talairach.m3z.inv.z.mgz',
], []),
('rmneck', ['mri/nu_noneck.mgz'], []),
('skull-lta', ['mri/transforms/talairach_with_skull_2.lta'], []),
('calabel', ['mri/aseg.auto_noCCseg.mgz',
'mri/aseg.auto.mgz',
'mri/aseg.mgz'], []),
('normalization2', ['mri/brain.mgz'], []),
('maskbfs', ['mri/brain.finalsurfs.mgz'], []),
('segmentation', ['mri/wm.seg.mgz',
'mri/wm.asegedit.mgz',
'mri/wm.mgz'], []),
('fill', ['mri/filled.mgz',
# 'scripts/ponscc.cut.log',
], []),
('tessellate', ['surf/lh.orig.nofix', 'surf/rh.orig.nofix'], []),
('smooth1', ['surf/lh.smoothwm.nofix', 'surf/rh.smoothwm.nofix'],
[]),
('inflate1', ['surf/lh.inflated.nofix', 'surf/rh.inflated.nofix'],
[]),
('qsphere', ['surf/lh.qsphere.nofix', 'surf/rh.qsphere.nofix'],
[]),
('fix', ['surf/lh.orig', 'surf/rh.orig'], []),
('white', ['surf/lh.white', 'surf/rh.white',
'surf/lh.curv', 'surf/rh.curv',
'surf/lh.area', 'surf/rh.area',
'label/lh.cortex.label', 'label/rh.cortex.label'], []),
('smooth2', ['surf/lh.smoothwm', 'surf/rh.smoothwm'], []),
('inflate2', ['surf/lh.inflated', 'surf/rh.inflated',
'surf/lh.sulc', 'surf/rh.sulc',
'surf/lh.inflated.H', 'surf/rh.inflated.H',
'surf/lh.inflated.K', 'surf/rh.inflated.K'], []),
]
_autorecon3_steps = [
('sphere', ['surf/lh.sphere', 'surf/rh.sphere'], []),
('surfreg', ['surf/lh.sphere.reg', 'surf/rh.sphere.reg'], []),
('jacobian_white', ['surf/lh.jacobian_white',
'surf/rh.jacobian_white'], []),
('avgcurv', ['surf/lh.avg_curv', 'surf/rh.avg_curv'], []),
('cortparc', ['label/lh.aparc.annot', 'label/rh.aparc.annot'], []),
('pial', ['surf/lh.pial', 'surf/rh.pial',
'surf/lh.curv.pial', 'surf/rh.curv.pial',
'surf/lh.area.pial', 'surf/rh.area.pial',
'surf/lh.thickness', 'surf/rh.thickness'], []),
('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'], []),
('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'], []),
('label-exvivo-ec', ['label/lh.entorhinal_exvivo.label',
'label/rh.entorhinal_exvivo.label'], []),
]
else:
_autorecon2_steps = [
('gcareg', ['mri/transforms/talairach.lta'], []),
('canorm', ['mri/norm.mgz'], []),
('careg', ['mri/transforms/talairach.m3z'], []),
('calabel', ['mri/aseg.auto_noCCseg.mgz',
'mri/aseg.auto.mgz',
'mri/aseg.mgz'], []),
('normalization2', ['mri/brain.mgz'], []),
('maskbfs', ['mri/brain.finalsurfs.mgz'], []),
('segmentation', ['mri/wm.seg.mgz',
'mri/wm.asegedit.mgz',
'mri/wm.mgz'], []),
('fill', ['mri/filled.mgz',
# 'scripts/ponscc.cut.log',
], []),
('tessellate', ['surf/lh.orig.nofix', 'surf/rh.orig.nofix'], []),
('smooth1', ['surf/lh.smoothwm.nofix', 'surf/rh.smoothwm.nofix'],
[]),
('inflate1', ['surf/lh.inflated.nofix', 'surf/rh.inflated.nofix'],
[]),
('qsphere', ['surf/lh.qsphere.nofix', 'surf/rh.qsphere.nofix'],
[]),
('fix', ['surf/lh.orig', 'surf/rh.orig'], []),
('white', ['surf/lh.white.preaparc', 'surf/rh.white.preaparc',
'surf/lh.curv', 'surf/rh.curv',
'surf/lh.area', 'surf/rh.area',
'label/lh.cortex.label', 'label/rh.cortex.label'], []),
('smooth2', ['surf/lh.smoothwm', 'surf/rh.smoothwm'], []),
('inflate2', ['surf/lh.inflated', 'surf/rh.inflated',
'surf/lh.sulc', 'surf/rh.sulc'], []),
('curvHK', ['surf/lh.white.H', 'surf/rh.white.H',
'surf/lh.white.K', 'surf/rh.white.K',
'surf/lh.inflated.H', 'surf/rh.inflated.H',
'surf/lh.inflated.K', 'surf/rh.inflated.K'], []),
('curvstats', ['stats/lh.curv.stats', 'stats/rh.curv.stats'], []),
]
_autorecon3_steps = [
('sphere', ['surf/lh.sphere', 'surf/rh.sphere'], []),
('surfreg', ['surf/lh.sphere.reg', 'surf/rh.sphere.reg'], []),
('jacobian_white', ['surf/lh.jacobian_white',
'surf/rh.jacobian_white'], []),
('avgcurv', ['surf/lh.avg_curv', 'surf/rh.avg_curv'], []),
('cortparc', ['label/lh.aparc.annot', 'label/rh.aparc.annot'], []),
('pial', ['surf/lh.pial', 'surf/rh.pial',
'surf/lh.curv.pial', 'surf/rh.curv.pial',
'surf/lh.area.pial', 'surf/rh.area.pial',
'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'], []),
('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'], []),
('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'], []),
('pctsurfcon', ['surf/lh.w-g.pct.mgh', 'surf/rh.w-g.pct.mgh'], []),
('hyporelabel', ['mri/aseg.presurf.hypos.mgz'], []),
('aparc2aseg', ['mri/aparc+aseg.mgz',
'mri/aparc.a2009s+aseg.mgz',
'mri/aparc.DKTatlas+aseg.mgz'], []),
('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',
'label/lh.entorhinal_exvivo.label',
'label/rh.entorhinal_exvivo.label'], []),
]

_steps = _autorecon1_steps + _autorecon2_steps + _autorecon3_steps

def _gen_subjects_dir(self):
return os.getcwd()
Expand Down Expand Up @@ -790,24 +888,21 @@ def cmdline(self):
subjects_dir = self.inputs.subjects_dir
if not isdefined(subjects_dir):
subjects_dir = self._gen_subjects_dir()
# cmd = cmd.replace(' -all ', ' -make all ')
iflogger.info('Overriding recon-all directive')

flags = []
directive = 'all'
for idx, step in enumerate(self._steps):
step, outfiles = step
if all([os.path.exists(os.path.join(subjects_dir,
self.inputs.subject_id, f)) for
f in outfiles]):
flags.append('-no%s' % step)
if idx > 4:
directive = 'autorecon2'
elif idx > 23:
directive = 'autorecon3'
else:
flags.append('-%s' % step)
cmd = cmd.replace(' -%s ' % self.inputs.directive, ' -%s ' % directive)
step, outfiles, infiles = step
flag = '-{}'.format(step)
noflag = '-no{}'.format(step)
if flag in cmd or noflag in cmd:
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)

iflogger.info('resume recon-all : %s' % cmd)
return cmd

Expand Down
13 changes: 13 additions & 0 deletions nipype/utils/filemanip.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -447,6 +447,19 @@ def list_to_filename(filelist):
else:
return filelist[0]


def check_depends(targets, dependencies):
"""Return true if all targets exist and are newer than all dependencies.

An OSError will be raised if there are missing dependencies.
"""
tgts = filename_to_list(targets)
deps = filename_to_list(dependencies)
return all(map(os.path.exists, tgts)) and \
min(map(os.path.getmtime, tgts)) > \
max(list(map(os.path.getmtime, deps)) + [0])


def save_json(filename, data):
"""Save data to a json file

Expand Down
Loading