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WIP Update ReconAll interface for v6
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‎nipype/interfaces/freesurfer/preprocess.py

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@@ -659,82 +659,86 @@ class ReconAll(CommandLine):
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_steps = [
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# autorecon1
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('motioncor', ['mri/rawavg.mgz', 'mri/orig.mgz']),
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('talairach', ['mri/transforms/talairach.auto.xfm',
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'mri/transforms/talairach.xfm']),
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('talairach', ['mri/orig_nu.mgz',
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'mri/transforms/talairach.auto.xfm',
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'mri/transforms/talairach.xfm',
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# 'mri/transforms/talairach_avi.log',
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]),
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('nuintensitycor', ['mri/nu.mgz']),
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('normalization', ['mri/T1.mgz']),
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('skullstrip',
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['mri/brainmask.auto.mgz',
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'mri/brainmask.mgz']),
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('skullstrip', ['mri/talairach_with_skull.lta',
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'mri/brainmask.auto.mgz',
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'mri/brainmask.mgz']),
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# autorecon2
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('gcareg', ['mri/transforms/talairach.lta']),
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('canorm', ['mri/norm.mgz']),
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('careg', ['mri/transforms/talairach.m3z']),
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('careginv', ['mri/transforms/talairach.m3z.inv.x.mgz',
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'mri/transforms/talairach.m3z.inv.y.mgz',
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'mri/transforms/talairach.m3z.inv.z.mgz']),
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('rmneck', ['mri/nu_noneck.mgz']),
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('skull-lta', ['mri/transforms/talairach_with_skull_2.lta']),
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('calabel',
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['mri/aseg.auto_noCCseg.mgz', 'mri/aseg.auto.mgz', 'mri/aseg.mgz']),
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('calabel', ['mri/aseg.auto_noCCseg.mgz',
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'mri/aseg.auto.mgz',
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'mri/aseg.mgz']),
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('normalization2', ['mri/brain.mgz']),
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('maskbfs', ['mri/brain.finalsurfs.mgz']),
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('segmentation', ['mri/wm.asegedit.mgz', 'mri/wm.mgz']),
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('fill', ['mri/filled.mgz']),
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('segmentation', ['mri/wm.seg.mgz',
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'mri/wm.asegedit.mgz',
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'mri/wm.mgz']),
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('fill', ['mri/filled.mgz',
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# 'scripts/ponscc.cut.log',
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]),
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('tessellate', ['surf/lh.orig.nofix', 'surf/rh.orig.nofix']),
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('smooth1', ['surf/lh.smoothwm.nofix', 'surf/rh.smoothwm.nofix']),
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('inflate1', ['surf/lh.inflated.nofix', 'surf/rh.inflated.nofix']),
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('qsphere', ['surf/lh.qsphere.nofix', 'surf/rh.qsphere.nofix']),
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('fix', ['surf/lh.orig', 'surf/rh.orig']),
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('white',
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['surf/lh.white',
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'surf/rh.white',
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'surf/lh.curv',
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'surf/rh.curv',
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'surf/lh.area',
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'surf/rh.area',
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'label/lh.cortex.label',
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'label/rh.cortex.label']),
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('white', ['surf/lh.white.preaparc', 'surf/rh.white.preaparc',
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'surf/lh.curv', 'surf/rh.curv',
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'surf/lh.area', 'surf/rh.area',
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'label/lh.cortex.label', 'label/rh.cortex.label']),
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('smooth2', ['surf/lh.smoothwm', 'surf/rh.smoothwm']),
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('inflate2',
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['surf/lh.inflated',
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'surf/rh.inflated',
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'surf/lh.sulc',
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'surf/rh.sulc',
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'surf/lh.inflated.H',
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'surf/rh.inflated.H',
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'surf/lh.inflated.K',
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'surf/rh.inflated.K']),
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('inflate2', ['surf/lh.inflated', 'surf/rh.inflated',
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'surf/lh.sulc', 'surf/rh.sulc']),
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('curvHK', ['surf/lh.white.H', 'surf/rh.white.H',
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'surf/lh.white.K', 'surf/rh.white.K',
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'surf/lh.inflated.H', 'surf/rh.inflated.H',
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'surf/lh.inflated.K', 'surf/rh.inflated.K']),
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('curvstats', ['stats/lh.curv.stats', 'stats/rh.curv.stats']),
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# autorecon3
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('sphere', ['surf/lh.sphere', 'surf/rh.sphere']),
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('surfreg', ['surf/lh.sphere.reg', 'surf/rh.sphere.reg']),
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('jacobian_white', ['surf/lh.jacobian_white',
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'surf/rh.jacobian_white']),
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('avgcurv', ['surf/lh.avg_curv', 'surf/rh.avg_curv']),
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('cortparc', ['label/lh.aparc.annot', 'label/rh.aparc.annot']),
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('pial',
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['surf/lh.pial',
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'surf/rh.pial',
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'surf/lh.curv.pial',
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'surf/rh.curv.pial',
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'surf/lh.area.pial',
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'surf/rh.area.pial',
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'surf/lh.thickness',
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'surf/rh.thickness']),
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('cortparc2', ['label/lh.aparc.a2009s.annot',
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'label/rh.aparc.a2009s.annot']),
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('parcstats2',
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['stats/lh.aparc.a2009s.stats',
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'stats/rh.aparc.a2009s.stats',
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'stats/aparc.annot.a2009s.ctab']),
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('pial', ['surf/lh.pial', 'surf/rh.pial',
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'surf/lh.curv.pial', 'surf/rh.curv.pial',
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'surf/lh.area.pial', 'surf/rh.area.pial',
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'surf/lh.thickness', 'surf/rh.thickness']),
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# TODO: Optional -T2pial / -FLAIRpial
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('cortribbon', ['mri/lh.ribbon.mgz', 'mri/rh.ribbon.mgz',
731717
'mri/ribbon.mgz']),
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('parcstats', ['stats/lh.aparc.astats', 'stats/rh.aparc.stats',
719+
'stats/aparc.annot.ctab']),
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('cortparc2', ['label/lh.aparc.a2009s.annot',
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'label/rh.aparc.a2009s.annot']),
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('parcstats2', ['stats/lh.aparc.a2009s.stats',
723+
'stats/rh.aparc.a2009s.stats',
724+
'stats/aparc.annot.a2009s.ctab']),
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('cortparc3', ['label/lh.aparc.DKTatlas.annot',
726+
'label/rh.aparc.DKTatlas.annot']),
727+
('parcstats3', ['stats/lh.aparc.DKTatlas.stats',
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'stats/rh.aparc.DKTatlas.stats',
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'stats/aparc.annot.DKTatlas.ctab']),
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('pctsurfcon', ['surf/lh.w-g.pct.mgh', 'surf/rh.w-g.pct.mgh']),
731+
('hyporelabel', ['mri/aseg.presurf.hypos.mgz']),
732+
('aparc2aseg', ['mri/aparc+aseg.mgz',
733+
'mri/aparc.a2009s+aseg.mgz',
734+
'mri/aparc.DKTatlas+aseg.mgz']),
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('apas2aseg', ['mri/aseg.mgz']), # XXX: Will not run because of calabel
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('segstats', ['stats/aseg.stats']),
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('aparc2aseg', ['mri/aparc+aseg.mgz', 'mri/aparc.a2009s+aseg.mgz']),
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('wmparc', ['mri/wmparc.mgz', 'stats/wmparc.stats']),
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('balabels', ['BA.ctab', 'BA.thresh.ctab']),
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('label-exvivo-ec', ['label/lh.entorhinal_exvivo.label',
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'label/rh.entorhinal_exvivo.label'])]
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('balabels', ['BA.ctab', 'BA.thresh.ctab',
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'label/lh.entorhinal_exvivo.label',
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'label/rh.entorhinal_exvivo.label']),
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]
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def _gen_subjects_dir(self):
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return os.getcwd()

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