Module Import alias Import alias Import alias Import alias Import alias identifier TryExcept body Import alias handlers ExceptHandler type NameLoad body Print Str Expr Call AttributeLoad NameLoad attr Num TryExcept body Import alias identifier handlers ExceptHandler type NameLoad body Print Str Expr Call AttributeLoad NameLoad attr Num FunctionDef arguments args defaults body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Str Index Num Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Str Index Num Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad NameLoad Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad NameLoad Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign TupleStore SubscriptStore NameLoad Index Num SubscriptStore NameLoad Index Num TupleLoad Num Num Assign NameStore Call AttributeLoad NameLoad attr Num For NameStore Call NameLoad Num body Assign SubscriptStore NameLoad Index NameLoad BinOpSub SubscriptLoad NameLoad Index BinOpAdd NameLoad Num SubscriptLoad NameLoad Index BinOpAdd NameLoad Num Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num NameLoad Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num Call NameLoad Call AttributeLoad NameLoad attr Num Num keyword Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Num For NameStore Call NameLoad Num Num Num body Assign SubscriptStore NameLoad Index BinOpSub NameLoad Num BinOpDiv BinOpSub SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index BinOpAdd NameLoad Num BinOpSub SubscriptLoad NameLoad Index BinOpAdd NameLoad Num SubscriptLoad NameLoad Index NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr BinOpSub Call NameLoad NameLoad Num For NameStore Call NameLoad BinOpSub Call NameLoad NameLoad Num body Assign SubscriptStore NameLoad Index NameLoad BinOpDiv BinOpSub SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index BinOpAdd NameLoad Num NameLoad Assign SubscriptStore NameLoad Index Num BinOpSub SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign SubscriptStore NameLoad Index Num BinOpSub SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign SubscriptStore NameLoad Index Num BinOpAdd SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign SubscriptStore NameLoad Index Num BinOpAdd SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign SubscriptStore NameLoad Index Num BinOpAdd SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign SubscriptStore NameLoad Index Num BinOpAdd SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign SubscriptStore NameLoad Index Num BinOpAdd SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign SubscriptStore NameLoad Index Num BinOpAdd SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign SubscriptStore NameLoad Index Num BinOpSub SubscriptLoad NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num BinOpSub SubscriptLoad NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num BinOpSub SubscriptLoad NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num BinOpSub SubscriptLoad NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num BinOpSub SubscriptLoad NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num BinOpSub SubscriptLoad NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num BinOpSub SubscriptLoad NameLoad Index Num Call NameLoad Num Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num SubscriptLoad NameLoad Slice Num Num Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num Call NameLoad Call AttributeLoad NameLoad attr Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num SubscriptLoad NameLoad Slice Num Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num SubscriptLoad NameLoad Slice Num Num Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num Call NameLoad Call AttributeLoad NameLoad attr Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num SubscriptLoad NameLoad Slice Num Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num Assign SubscriptStore NameLoad Index Num Call NameLoad Num For NameStore Call NameLoad Call NameLoad NameLoad body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Num Num Num SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num Num NameLoad Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad NameLoad For NameStore Call NameLoad Call NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad Call NameLoad BinOpMult BinOpSub SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad NameLoad For NameStore Call NameLoad Call NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad Call NameLoad BinOpAdd SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad Assign NameStore Num Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr CompareGt NameLoad Num For NameStore SubscriptLoad NameLoad Slice body Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Num For NameStore Call NameLoad Call AttributeLoad NameLoad attr NameLoad BinOpSub Call AttributeLoad NameLoad attr NameLoad Num Num body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr CompareGt SubscriptLoad NameLoad ExtSlice Slice Slice Index NameLoad Num Assign NameStore BinOpDiv BinOpSub NameLoad NameLoad NameLoad Assign NameStore Call NameLoad BinOpAdd SubscriptLoad NameLoad Index NameLoad NameLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad Assign SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad NameLoad NameLoad Assign NameStore BinOpAdd NameLoad Num Expr Call AttributeLoad NameLoad attr Str Print Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad If CompareLtE NameLoad Num body Assign NameStore BinOpAdd BinOpAdd Str Call NameLoad NameLoad Str orelse Assign NameStore BinOpAdd BinOpAdd Str Call NameLoad BinOpSub NameLoad Num Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Print BinOpAdd Str NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr NameLoad For NameStore Call NameLoad BinOpAdd Call NameLoad Call AttributeLoad NameLoad attr NameLoad Num BinOpAdd Call NameLoad Call AttributeLoad NameLoad attr NameLoad Num body Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr CompareEq NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign SubscriptStore NameLoad Index BinOpSub NameLoad Num BinOpAdd Call AttributeLoad NameLoad attr NameLoad Call NameLoad BinOpDiv BinOpSub Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr NameLoad Num Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Return BinOpDiv Call AttributeLoad NameLoad attr BinOpDiv UnaryOpUSub BinOpMult BinOpSub NameLoad NameLoad BinOpSub NameLoad NameLoad BinOpMult BinOpMult Num NameLoad NameLoad Call AttributeLoad NameLoad attr BinOpMult BinOpMult BinOpMult Num AttributeLoad NameLoad attr NameLoad NameLoad decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A os N/A getopt N/A commands N/A sys N/A matplotlib.pyplot plt N/A N/A N/A nibabel N/A N/A N/A ImportError N/A N/A --- nibabel not installed! Exit program. --- N/A N/A N/A sys exit 2 N/A N/A N/A numpy np N/A N/A N/A ImportError N/A N/A --- numpy not installed! Exit program. --- N/A N/A N/A sys exit 2 main N/A N/A N/A N/A N/A N/A status path_sct N/A N/A commands getstatusoutput echo $SCT_DIR N/A fname_template_vertebral_level N/A path_sct /data/template/MNI-Poly-AMU_level.nii.gz N/A fname_template_vertebral_cord N/A path_sct /data/template/MNI-Poly-AMU_cord.nii.gz N/A vertebral_level_file N/A N/A nibabel load fname_template_vertebral_level N/A vertebral_cord_file N/A N/A nibabel load fname_template_vertebral_cord N/A vertebral_level_image N/A N/A vertebral_level_file get_data N/A vertebral_cord_image N/A N/A vertebral_cord_file get_data N/A hdr_vertebral_level N/A N/A vertebral_level_file get_header N/A hdr_vertebral_cord N/A N/A vertebral_cord_file get_header N/A z_size_vertebral_level N/A N/A hdr_vertebral_level N/A pixdim N/A 3 N/A z_size_vertebral_cord N/A N/A hdr_vertebral_cord N/A pixdim N/A 3 N/A vertebral_levels N/A find_mid_point_vertebral_level vertebral_level_image N/A vertebral_Mu N/A N/A np zeros N/A len vertebral_levels N/A vertebral_Sigma N/A N/A np zeros N/A len vertebral_levels N/A N/A N/A vertebral_Mu N/A 0 N/A vertebral_Sigma N/A 0 N/A 0 0 N/A N/A N/A vertebral_Mu N/A 1 N/A vertebral_Sigma N/A 1 N/A 0 0 N/A N/A N/A vertebral_Mu N/A 2 N/A vertebral_Sigma N/A 2 N/A 69.99 4.58 N/A N/A N/A vertebral_Mu N/A 3 N/A vertebral_Sigma N/A 3 N/A 86.11 5.35 N/A N/A N/A vertebral_Mu N/A 4 N/A vertebral_Sigma N/A 4 N/A 101.16 6.33 N/A N/A N/A vertebral_Mu N/A 5 N/A vertebral_Sigma N/A 5 N/A 115.54 7.15 N/A N/A N/A vertebral_Mu N/A 6 N/A vertebral_Sigma N/A 6 N/A 130.08 8.25 N/A N/A N/A vertebral_Mu N/A 7 N/A vertebral_Sigma N/A 7 N/A 0 0 N/A N/A N/A vertebral_Mu N/A 8 N/A vertebral_Sigma N/A 8 N/A 0 0 N/A N/A N/A vertebral_Mu N/A 9 N/A vertebral_Sigma N/A 9 N/A 0 0 N/A N/A N/A vertebral_Mu N/A 10 N/A vertebral_Sigma N/A 10 N/A 0 0 N/A N/A N/A vertebral_Mu N/A 11 N/A vertebral_Sigma N/A 11 N/A 0 0 N/A N/A N/A vertebral_Mu N/A 12 N/A vertebral_Sigma N/A 12 N/A 0 0 N/A spinal_Mu N/A N/A np zeros N/A len vertebral_levels N/A spinal_Sigma N/A N/A np zeros N/A len vertebral_levels N/A N/A N/A spinal_Mu N/A 0 N/A spinal_Sigma N/A 0 N/A 0 0 N/A N/A N/A spinal_Mu N/A 1 N/A spinal_Sigma N/A 1 N/A 0 0 N/A N/A N/A spinal_Mu N/A 2 N/A spinal_Sigma N/A 2 N/A 51.46 3.15 N/A N/A N/A spinal_Mu N/A 3 N/A spinal_Sigma N/A 3 N/A 65.68 3.96 N/A N/A N/A spinal_Mu N/A 4 N/A spinal_Sigma N/A 4 N/A 81.08 5.15 N/A N/A N/A spinal_Mu N/A 5 N/A spinal_Sigma N/A 5 N/A 95.39 5.68 N/A N/A N/A spinal_Mu N/A 6 N/A spinal_Sigma N/A 6 N/A 109.33 6.05 N/A N/A N/A spinal_Mu N/A 7 N/A spinal_Sigma N/A 7 N/A 122.77 7.03 N/A N/A N/A spinal_Mu N/A 8 N/A spinal_Sigma N/A 8 N/A 0 0 N/A N/A N/A spinal_Mu N/A 9 N/A spinal_Sigma N/A 9 N/A 0 0 N/A N/A N/A spinal_Mu N/A 10 N/A spinal_Sigma N/A 10 N/A 0 0 N/A N/A N/A spinal_Mu N/A 11 N/A spinal_Sigma N/A 11 N/A 0 0 N/A N/A N/A spinal_Mu N/A 12 N/A spinal_Sigma N/A 12 N/A 0 0 N/A spinal_vertebral_dist N/A N/A np zeros 5 N/A i N/A range 5 N/A N/A N/A spinal_vertebral_dist N/A i N/A N/A vertebral_Mu N/A N/A i 2 N/A spinal_Mu N/A N/A i 2 N/A popt_spinal_vertebral N/A N/A np polyfit N/A N/A np arange 3 8 spinal_vertebral_dist 1 N/A P_fit_spinal_vertebral_dist N/A N/A np poly1d popt_spinal_vertebral N/A N/A N/A plt plot N/A N/A np arange 0 15 N/A P_fit_spinal_vertebral_dist N/A N/A np arange 0 15 marker + N/A N/A N/A plt plot N/A N/A np arange 3 8 spinal_vertebral_dist marker o linestyle None N/A N/A N/A plt title Spinal-Vertebral distances N/A N/A N/A plt show N/A conversion_factor N/A N/A np zeros 4 N/A i N/A range 2 6 1 N/A N/A N/A conversion_factor N/A N/A i 2 N/A N/A N/A vertebral_levels N/A i N/A vertebral_levels N/A N/A i 1 N/A N/A vertebral_Mu N/A N/A i 1 N/A vertebral_Mu N/A i N/A average_conversion_factor N/A N/A np mean conversion_factor N/A delta_vertebral_levels N/A N/A np zeros N/A N/A len vertebral_levels 1 N/A i N/A range N/A N/A len vertebral_levels 1 N/A N/A N/A delta_vertebral_levels N/A i N/A N/A N/A vertebral_levels N/A i N/A vertebral_levels N/A N/A i 1 average_conversion_factor N/A N/A vertebral_Mu N/A 0 N/A N/A vertebral_Mu N/A 1 N/A delta_vertebral_levels N/A 0 N/A N/A vertebral_Mu N/A 1 N/A N/A vertebral_Mu N/A 2 N/A delta_vertebral_levels N/A 1 N/A N/A vertebral_Mu N/A 7 N/A N/A vertebral_Mu N/A 6 N/A delta_vertebral_levels N/A 6 N/A N/A vertebral_Mu N/A 8 N/A N/A vertebral_Mu N/A 7 N/A delta_vertebral_levels N/A 7 N/A N/A vertebral_Mu N/A 9 N/A N/A vertebral_Mu N/A 8 N/A delta_vertebral_levels N/A 8 N/A N/A vertebral_Mu N/A 10 N/A N/A vertebral_Mu N/A 9 N/A delta_vertebral_levels N/A 9 N/A N/A vertebral_Mu N/A 11 N/A N/A vertebral_Mu N/A 10 N/A delta_vertebral_levels N/A 10 N/A N/A vertebral_Mu N/A 12 N/A N/A vertebral_Mu N/A 11 N/A delta_vertebral_levels N/A 11 N/A N/A spinal_Mu N/A 0 N/A N/A vertebral_Mu N/A 0 N/A P_fit_spinal_vertebral_dist 1 N/A N/A spinal_Mu N/A 1 N/A N/A vertebral_Mu N/A 1 N/A P_fit_spinal_vertebral_dist 2 N/A N/A spinal_Mu N/A 8 N/A N/A vertebral_Mu N/A 8 N/A P_fit_spinal_vertebral_dist 9 N/A N/A spinal_Mu N/A 9 N/A N/A vertebral_Mu N/A 9 N/A P_fit_spinal_vertebral_dist 10 N/A N/A spinal_Mu N/A 10 N/A N/A vertebral_Mu N/A 10 N/A P_fit_spinal_vertebral_dist 11 N/A N/A spinal_Mu N/A 11 N/A N/A vertebral_Mu N/A 11 N/A P_fit_spinal_vertebral_dist 12 N/A N/A spinal_Mu N/A 12 N/A N/A vertebral_Mu N/A 12 N/A P_fit_spinal_vertebral_dist 13 N/A popt_vertebral_sigma N/A N/A np polyfit N/A N/A np arange 3 8 N/A vertebral_Sigma N/A 2 7 1 N/A P_fit_vertebral_sigma N/A N/A np poly1d popt_vertebral_sigma N/A N/A N/A plt plot N/A N/A np arange 0 14 N/A P_fit_vertebral_sigma N/A N/A np arange 0 14 marker + N/A N/A N/A plt title Vertebral_sigma N/A N/A N/A plt plot N/A N/A np arange 3 8 N/A vertebral_Sigma N/A 2 7 marker o linestyle None N/A N/A N/A plt show N/A popt_spinal_sigma N/A N/A np polyfit N/A N/A np arange 3 9 N/A spinal_Sigma N/A 2 8 1 N/A P_fit_spinal_sigma N/A N/A np poly1d popt_spinal_sigma N/A N/A N/A plt plot N/A N/A np arange 0 14 N/A P_fit_spinal_sigma N/A N/A np arange 0 14 marker + N/A N/A N/A plt title Spinal_sigma N/A N/A N/A plt plot N/A N/A np arange 3 9 N/A spinal_Sigma N/A 2 8 marker o linestyle None N/A N/A N/A plt show N/A N/A vertebral_Sigma N/A 1 N/A P_fit_vertebral_sigma 0 N/A N/A vertebral_Sigma N/A 0 N/A P_fit_vertebral_sigma 1 N/A N/A vertebral_Sigma N/A 7 N/A P_fit_vertebral_sigma 8 N/A N/A vertebral_Sigma N/A 8 N/A P_fit_vertebral_sigma 9 N/A N/A vertebral_Sigma N/A 9 N/A P_fit_vertebral_sigma 10 N/A N/A vertebral_Sigma N/A 10 N/A P_fit_vertebral_sigma 11 N/A N/A vertebral_Sigma N/A 11 N/A P_fit_vertebral_sigma 12 N/A N/A vertebral_Sigma N/A 12 N/A P_fit_vertebral_sigma 13 N/A N/A spinal_Sigma N/A 1 N/A P_fit_spinal_sigma 2 N/A N/A spinal_Sigma N/A 0 N/A P_fit_spinal_sigma 1 N/A N/A spinal_Sigma N/A 8 N/A P_fit_spinal_sigma 9 N/A N/A spinal_Sigma N/A 9 N/A P_fit_spinal_sigma 10 N/A N/A spinal_Sigma N/A 10 N/A P_fit_spinal_sigma 11 N/A N/A spinal_Sigma N/A 11 N/A P_fit_spinal_sigma 12 N/A N/A spinal_Sigma N/A 12 N/A P_fit_spinal_sigma 13 N/A i N/A range N/A len vertebral_levels N/A N/A y N/A gaussian N/A N/A np arange 0 500 0.1 N/A spinal_Mu N/A i N/A spinal_Sigma N/A i N/A N/A N/A plt plot N/A N/A np arange 0 500 0.1 y N/A N/A N/A plt title Mean Distance from the PMJ to the centre of each Nerve Rootlet Segment N/A N/A N/A plt show N/A spinal_vertebral_distances N/A N/A np zeros N/A len vertebral_levels N/A i N/A range N/A len vertebral_levels N/A N/A N/A spinal_vertebral_distances N/A i N/A round N/A N/A N/A vertebral_Mu N/A i N/A spinal_Mu N/A i average_conversion_factor N/A spinal_levels N/A N/A np zeros N/A len vertebral_levels N/A i N/A range N/A len vertebral_levels N/A N/A N/A spinal_levels N/A i N/A int N/A N/A vertebral_levels N/A i N/A spinal_vertebral_distances N/A i N/A k 0 N/A N/A X Y Z N/A N/A np where N/A vertebral_cord_image 0 N/A i N/A spinal_levels N/A N/A N/A template_spinal_image N/A N/A vertebral_cord_image copy N/A count 0 N/A j N/A range N/A N/A np amax Z N/A N/A N/A np amin Z 1 -1 N/A N/A N/A x y N/A N/A np where N/A N/A vertebral_cord_image N/A N/A N/A N/A j 0 N/A diff N/A N/A i j average_conversion_factor N/A value N/A gaussian N/A N/A spinal_Mu N/A k diff N/A spinal_Mu N/A k N/A spinal_Sigma N/A k N/A N/A template_spinal_image N/A N/A x y j value N/A k N/A k 1 N/A N/A N/A hdr_vertebral_cord set_data_dtype uint8 N/A 
Write NIFTI volumes... N/A img N/A N/A nibabel Nifti1Image template_spinal_image None hdr_vertebral_cord N/A N/A k 8 N/A N/A file_name N/A N/A spinal_level_C N/A str k .nii.gz N/A N/A file_name N/A N/A spinal_level_T N/A str N/A k 8 .nii.gz N/A N/A N/A nibabel save img file_name N/A N/A .. File created: file_name N/A find_mid_point_vertebral_level N/A N/A data N/A N/A N/A vertebral_levels N/A N/A np zeros N/A int N/A N/A np amax data N/A i N/A range N/A N/A int N/A N/A np amin data 1 N/A N/A int N/A N/A np amax data 1 N/A N/A N/A x y z N/A N/A np where N/A data i N/A z N/A N/A np sort z N/A N/A vertebral_levels N/A N/A i 1 N/A N/A N/A np amin z N/A round N/A N/A N/A N/A np amax z N/A N/A np amin z 2 N/A vertebral_levels N/A gaussian N/A N/A x mu sig N/A N/A N/A N/A N/A N/A np exp N/A N/A N/A N/A x mu N/A x mu N/A N/A 2 sig sig N/A N/A np sqrt N/A N/A N/A 2 N/A np pi sig sig N/A N/A N/A __name__ __main__ N/A N/A N/A main