Module ImportFrom alias ImportFrom alias Import alias identifier Import alias identifier Import alias identifier Import alias identifier Import alias identifier Import alias identifier Import alias identifier Import alias identifier ImportFrom alias alias alias Import alias Import alias ImportFrom alias Import alias Assign NameStore Call AttributeLoad NameLoad attr NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr Str Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Num keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr keyword NameLoad decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam defaults body Expr Str Expr Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Str Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Assign NameStore Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str keyword NameLoad For NameStore NameLoad body For NameStore NameLoad body If CompareNotEq NameLoad Str body Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad If UnaryOpNot AttributeLoad AttributeLoad NameLoad attr attr body Assign AttributeStore AttributeLoad NameLoad attr attr BinOpAdd Call NameLoad Call AttributeLoad NameLoad attr Str Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad AttributeLoad NameLoad attr attr keyword Str If BoolOpAnd CompareNotEq AttributeLoad AttributeLoad NameLoad attr attr Str CompareNotEq AttributeLoad AttributeLoad NameLoad attr attr Str body Expr Call AttributeLoad NameLoad attr BinOpAdd Str AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr If CompareEq AttributeLoad AttributeLoad NameLoad attr attr Num body Assign NameStore Num orelse Assign NameStore BinOpSub AttributeLoad AttributeLoad NameLoad attr attr Num If BoolOpAnd CompareEq NameLoad Num AttributeLoad AttributeLoad NameLoad attr attr body Expr Call NameLoad Str Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore NameLoad If CompareEq AttributeLoad AttributeLoad NameLoad attr attr Str body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore ListLoad For NameStore NameLoad body For NameStore Call NameLoad Call NameLoad SubscriptLoad NameLoad Index NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index NameLoad Assign NameStore BinOpAdd BinOpAdd BinOpAdd AttributeLoad NameLoad attr Str AttributeLoad AttributeLoad NameLoad attr attr Str Assign NameStore Call AttributeLoad NameLoad attr BinOpAdd ListLoad NameLoad NameLoad keyword NameLoad keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr For NameStore AttributeLoad AttributeLoad NameLoad attr attr body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad AttributeLoad NameLoad attr attr Str body Assign NameStore NameLoad Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index Num Index Num For NameStore NameLoad body For NameStore Call NameLoad Call NameLoad SubscriptLoad NameLoad Index NameLoad body If CompareLt Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index NameLoad orelse Expr Call NameLoad BinOpAdd Str Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr Expr Call NameLoad Str Expr Call AttributeLoad NameLoad attr For NameStore NameLoad body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore Call NameLoad NameLoad For NameStore Call NameLoad NameLoad body Expr Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr keyword Str For NameStore NameLoad body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore Call NameLoad NameLoad For NameStore Call NameLoad BinOpSub NameLoad Num body If CompareEq AttributeLoad AttributeLoad NameLoad attr attr Str body Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index BinOpAdd NameLoad Num keyword AttributeLoad AttributeLoad NameLoad attr attr keyword AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad AttributeLoad NameLoad attr attr Str body Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index BinOpAdd NameLoad Num keyword AttributeLoad AttributeLoad NameLoad attr attr keyword AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index BinOpAdd NameLoad Num keyword SubscriptLoad NameLoad Index BinOpAdd NameLoad Num keyword ListLoad Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Str Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr SubscriptLoad NameLoad Index BinOpAdd NameLoad Num Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index BinOpAdd NameLoad Num attr SubscriptLoad NameLoad Index NameLoad If UnaryOpNot NameLoad body Expr Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index BinOpAdd NameLoad Num attr SubscriptLoad NameLoad Index NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num If AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore ListLoad For NameStore NameLoad body If CompareGtE NameLoad Num body Expr Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index NameLoad orelse Assign NameStore BinOpSub Call NameLoad SubscriptLoad NameLoad Index NameLoad Num Expr Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad AttributeLoad NameLoad attr keyword AttributeLoad AttributeLoad NameLoad attr attr keyword NameLoad keyword NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr orelse If BoolOpAnd AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr body If BoolOpOr UnaryOpNot Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr UnaryOpNot Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr body Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr keyword AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Str Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr keyword NameLoad orelse Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Str Assign NameStore NameLoad Expr Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr decorator_list decorator_list If CompareEq NameLoad Str body Assign NameStore Call NameLoad Expr Call AttributeLoad NameLoad attr
N/A __future__ print_function pydpiper.application AbstractApplication N/A atoms_and_modules.registration_functions rf N/A atoms_and_modules.registration_file_handling rfh N/A atoms_and_modules.minc_modules mm N/A atoms_and_modules.minc_atoms ma N/A atoms_and_modules.LSQ6 lsq6 N/A atoms_and_modules.LSQ12 lsq12 N/A atoms_and_modules.NLIN nlin N/A atoms_and_modules.stats_tools st os.path abspath isdir isfile N/A logging N/A sys datetime date N/A csv N/A logger N/A N/A logging getLogger __name__ addRegChainArgumentGroup N/A N/A parser N/A N/A N/A option group for the command line argument parser N/A group N/A N/A parser add_argument_group Registration-chain options Options for registering consecutive timepoints of longitudinal data. N/A N/A N/A group add_argument --avg-time-point dest avg_time_point type int default 1 help Time point averaged prior to this registration to get common nlin space.If you want to use the last time point from each of your input files, (they might differ per input file) specify -1. [Default = %(default)s] N/A N/A N/A group add_argument --common-space-name dest common_name type str default common help Option to specify a name for the common space. This is useful for the creation of more readable output file names. Default is common. Note that the common space is the one created by an iterative group-wise registration, either within this code or one that was run previously. N/A N/A N/A group add_argument --run-groupwise dest run_groupwise action store_true help Run an iterative, groupwise registration (MBM) on the specified average  time point. [Default] N/A N/A N/A group add_argument --no-run-groupwise dest run_groupwise action store_false help If specified, do not run a groupwise registration on the specified average time point [Opposite of --run-groupwise.]. If an iterative group-wise registration was run previously, the average and transforms from that registration can be accessed using the --MBM-directory and --nlin-average options. (See below.) N/A N/A N/A group add_argument --MBM-directory dest mbm_dir type str default None help _processed directory from MBM used to average specified time point  N/A N/A N/A group add_argument --nlin-average dest nlin_avg type str default None help Final nlin average from MBM run. N/A N/A N/A parser set_defaults run_groupwise True N/A RegistrationChain N/A AbstractApplication N/A setup_options N/A N/A self N/A N/A N/A Add option groups from specific modules N/A N/A addRegChainArgumentGroup N/A self parser N/A N/A N/A rf addGenRegArgumentGroup N/A self parser N/A N/A N/A lsq6 addLSQ6ArgumentGroup N/A self parser N/A N/A N/A lsq12 addLSQ12ArgumentGroup N/A self parser N/A N/A N/A nlin addNlinRegArgumentGroup N/A self parser N/A N/A N/A st addStatsArguments N/A self parser N/A setup_appName N/A N/A self N/A N/A N/A appName Registration-chain N/A appName N/A run N/A N/A self N/A N/A N/A all_input_files N/A N/A fileList N/A open N/A N/A self args N/A 0 rb N/A subjectList N/A N/A csv reader fileList delimiter , skipinitialspace True N/A subjLine subjectList N/A N/A subj subjLine N/A N/A N/A subj N/A N/A N/A N/A all_input_files append subj N/A N/A N/A rf checkInputFiles all_input_files N/A N/A N/A N/A self options pipeline_name N/A N/A N/A N/A self options pipeline_name N/A N/A str N/A N/A date today _pipeline N/A dirs N/A N/A rf setupDirectories N/A self outputDir N/A N/A self options pipeline_name module ALL N/A N/A N/A N/A N/A self options reg_method minctracc N/A N/A N/A self options reg_method mincANTS N/A N/A N/A N/A logger error N/A Incorrect registration method specified:  N/A N/A self options reg_method N/A N/A N/A sys exit N/A N/A N/A N/A self options avg_time_point -1 N/A N/A avgTime -1 N/A N/A avgTime N/A N/A N/A self options avg_time_point 1 N/A N/A N/A avgTime -1 N/A N/A self options run_groupwise N/A N/A N/A print 
The groupwise registration will be run using the last time points for each of the input files.
 N/A subjects N/A N/A rf setupSubjectHash N/A N/A self args N/A 0 dirs N/A N/A self options mask_dir N/A resolutionForGroupWiseRegistration None N/A N/A N/A N/A self options input_space native N/A N/A N/A initModel targetPipeFH N/A N/A rf setInitialTarget N/A N/A self options init_model N/A N/A self options lsq6_target N/A dirs lsq6Dir N/A self outputDir N/A N/A self options pipeline_name N/A inputFiles N/A N/A subj subjects N/A N/A i N/A range N/A len N/A subjects N/A subj N/A N/A N/A N/A inputFiles append N/A N/A subjects N/A subj N/A i N/A montageBeforeRegistration N/A N/A N/A N/A self outputDir / N/A N/A self options pipeline_name _quality_control_target_and_inputfiles.png N/A initialVerificationImages N/A N/A mm createQualityControlImages N/A N/A targetPipeFH inputFiles montageOutPut montageBeforeRegistration message at the very start of the registration. N/A N/A N/A N/A self pipeline addPipeline N/A initialVerificationImages p N/A runLSQ6NucInorm N/A N/A lsq6 LSQ6NUCInorm inputFiles targetPipeFH initModel N/A dirs lsq6Dir N/A self options N/A lsq6Stage N/A N/A runLSQ6NucInorm p stages N/A N/A N/A N/A N/A lsq6Stage inputFiles append montageBeforeRegistration N/A N/A N/A N/A self pipeline addPipeline N/A runLSQ6NucInorm p N/A N/A N/A N/A N/A self options input_space lsq6 N/A N/A initModel None N/A resolutionForGroupWiseRegistration N/A N/A rf getFinestResolution N/A N/A subjects N/A 0 N/A 0 N/A subj subjects N/A N/A i N/A range N/A len N/A subjects N/A subj N/A N/A N/A N/A N/A rf getFinestResolution N/A N/A subjects N/A subj N/A i resolutionForGroupWiseRegistration N/A N/A resolutionForGroupWiseRegistration N/A N/A rf getFinestResolution N/A N/A subjects N/A subj N/A i N/A N/A N/A print N/A Only native and lsq6 are allowed as input_space options for the registration chain. You specified:  N/A str N/A N/A self options input_space N/A N/A print Exiting... N/A N/A N/A sys exit N/A subjKey subjects N/A N/A s N/A subjects N/A subjKey N/A count N/A len s N/A i N/A range count N/A N/A N/A N/A N/A s N/A i newGroup groupName chain N/A subjKey subjects N/A N/A s N/A subjects N/A subjKey N/A count N/A len s N/A i N/A range N/A count 1 N/A N/A N/A N/A N/A self options reg_method mincANTS N/A N/A register N/A N/A mm LSQ12ANTSNlin N/A s N/A i N/A s N/A N/A i 1 lsq12_protocol N/A N/A self options lsq12_protocol nlin_protocol N/A N/A self options nlin_protocol N/A N/A N/A N/A self pipeline addPipeline N/A register p N/A N/A N/A N/A N/A self options reg_method minctracc N/A N/A hm N/A N/A mm HierarchicalMinctracc N/A s N/A i N/A s N/A N/A i 1 lsq12_protocol N/A N/A self options lsq12_protocol nlin_protocol N/A N/A self options nlin_protocol N/A N/A N/A N/A self pipeline addPipeline N/A hm p N/A resample N/A N/A ma mincresample N/A s N/A i N/A s N/A N/A i 1 likeFile N/A s N/A N/A i 1 argArray N/A -sinc N/A N/A N/A N/A self pipeline addStage resample N/A Invert transforms for use later in stats N/A lastXfm N/A N/A N/A s N/A i getLastXfm N/A s N/A N/A i 1 N/A inverseXfm N/A N/A N/A s N/A N/A i 1 getLastXfm N/A s N/A i N/A N/A inverseXfm N/A N/A invert xfm and calculate N/A xi N/A N/A ma xfmInvert lastXfm FH N/A s N/A i N/A N/A N/A N/A self pipeline addStage xi N/A N/A N/A N/A s N/A N/A i 1 addAndSetXfmToUse N/A s N/A i N/A N/A xi outputFiles N/A 0 N/A N/A N/A self options run_groupwise N/A N/A inputs N/A N/A s subjects N/A N/A N/A avgTime 0 N/A N/A N/A N/A inputs append N/A N/A subjects N/A s N/A avgTime N/A N/A lastTimePoint N/A N/A len N/A subjects N/A s 1 N/A N/A N/A inputs append N/A N/A subjects N/A s N/A lastTimePoint N/A lsq12Nlin N/A N/A mm FullIterativeLSQ12Nlin inputs dirs N/A self options avgPrefix N/A N/A self options common_name initModel initModel fileResolution resolutionForGroupWiseRegistration N/A N/A N/A N/A self pipeline addPipeline N/A lsq12Nlin p N/A nlinFH N/A lsq12Nlin nlinFH N/A N/A N/A N/A N/A self options mbm_dir N/A N/A self options nlin_avg N/A N/A N/A N/A N/A isdir N/A N/A self options mbm_dir N/A N/A isfile N/A N/A self options nlin_avg N/A N/A N/A N/A logger error The specified MBM-directory or nlin-average do not exist. N/A N/A N/A logger error N/A Specified MBM-directory:  N/A abspath N/A N/A self options mbm_dir N/A N/A N/A logger error N/A Specified nlin average:  N/A abspath N/A N/A self options nlin_avg N/A N/A N/A sys exit N/A nlinFH N/A N/A rfh RegistrationPipeFH N/A abspath N/A N/A self options nlin_avg basedir N/A dirs processedDir N/A N/A N/A rf getXfms nlinFH subjects lsq6 N/A abspath N/A N/A self options mbm_dir time avgTime N/A N/A N/A N/A logger info MBM directory and nlin_average not specified. N/A N/A N/A logger info Calculating registration chain only N/A nlinFH None N/A Now that all registration is complete, calculate stats, concat transforms and resample N/A car N/A N/A mm LongitudinalStatsConcatAndResample subjects avgTime nlinFH N/A N/A self options stats_kernels N/A N/A self options common_name N/A N/A N/A N/A self pipeline addPipeline N/A car p N/A N/A N/A N/A __name__ __main__ N/A N/A application N/A RegistrationChain N/A N/A N/A application start