diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py index cf4e97c9c9..2b62d155e3 100644 --- a/nipype/interfaces/freesurfer/preprocess.py +++ b/nipype/interfaces/freesurfer/preprocess.py @@ -1081,6 +1081,7 @@ class ReconAll(CommandLine): # # [0] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3 # [1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 + # [2] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0#ReconAllTableStable7.1.1 _autorecon1_steps = [ ("motioncor", ["mri/rawavg.mgz", "mri/orig.mgz"], []), ( @@ -1210,7 +1211,7 @@ class ReconAll(CommandLine): ("wmparc", ["mri/wmparc.mgz", "stats/wmparc.stats"], []), ("balabels", ["label/BA.ctab", "label/BA.thresh.ctab"], []), ] - else: + elif Info.looseversion() < LooseVersion("7.0.0"): _autorecon2_volonly_steps = [ ("gcareg", ["mri/transforms/talairach.lta"], []), ("canorm", ["mri/norm.mgz"], []), @@ -1322,6 +1323,124 @@ class ReconAll(CommandLine): [], ), ] + else: + _autorecon2_volonly_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.presurf.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', + ], + [], + ), + ] + _autorecon2_lh_steps = [ + ("tessellate", ["surf/lh.orig.nofix"], []), + ("smooth1", ["surf/lh.smoothwm.nofix"], []), + ("inflate1", ["surf/lh.inflated.nofix"], []), + ("qsphere", ["surf/lh.qsphere.nofix"], []), + ("fix", ["surf/lh.inflated", "surf/lh.orig"], []), + ( + "white", + [ + "surf/lh.white.preaparc", + "surf/lh.curv", + "surf/lh.area", + "label/lh.cortex.label", + ], + [], + ), + ("smooth2", ["surf/lh.smoothwm"], []), + ("inflate2", ["surf/lh.inflated", "surf/lh.sulc"], []), + ( + "curvHK", + [ + "surf/lh.white.H", + "surf/lh.white.K", + "surf/lh.inflated.H", + "surf/lh.inflated.K", + ], + [], + ), + ("curvstats", ["stats/lh.curv.stats"], []), + ] + _autorecon3_lh_steps = [ + ("sphere", ["surf/lh.sphere"], []), + ("surfreg", ["surf/lh.sphere.reg"], []), + ("jacobian_white", ["surf/lh.jacobian_white"], []), + ("avgcurv", ["surf/lh.avg_curv"], []), + ("cortparc", ["label/lh.aparc.annot"], []), + ( + "pial", + [ + "surf/lh.pial", + "surf/lh.curv.pial", + "surf/lh.area.pial", + "surf/lh.thickness", + "surf/lh.white", + ], + [], + ), + ("parcstats", ["stats/lh.aparc.stats"], []), + ("cortparc2", ["label/lh.aparc.a2009s.annot"], []), + ("parcstats2", ["stats/lh.aparc.a2009s.stats"], []), + ("cortparc3", ["label/lh.aparc.DKTatlas.annot"], []), + ("parcstats3", ["stats/lh.aparc.DKTatlas.stats"], []), + ("pctsurfcon", ["surf/lh.w-g.pct.mgh", "stats/lh.w-g.pct.stats"], []), + ] + _autorecon3_added_steps = [ + ( + "cortribbon", + ["mri/lh.ribbon.mgz", "mri/rh.ribbon.mgz", "mri/ribbon.mgz"], + [], + ), + ("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"], []), + # 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", + "label/lh.perirhinal_exvivo.label", + "label/rh.perirhinal_exvivo.label", + ], + [], + ), + ] # Fill out autorecon2 steps _autorecon2_rh_steps = [