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parse_fs_lt_log.py - parse FreeSurfer labeltable log file
Get labeltable indices from a rank log file, such as:
aparc+aseg_rank.niml.lt.log
usage: parse_fs_lt_log.py -logfile aparc+aseg_rank.niml.lt.log \
-labels CC_Posterior CC_Mid_Posterior
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examples:
Example 0: common usage - simply get original indices for aparc+aseg.nii
parse_fs_lt_log.py -logfile aparc+aseg_rank.niml.lt.log \
-labels FS_white_matter -verb 0 -show_orig
Example 1: get known FreeSurfer labels
parse_fs_lt_log.py -logfile aparc+aseg_rank.niml.lt.log \
-labels FS_white_matter
parse_fs_lt_log.py -logfile aparc+aseg_rank.niml.lt.log \
-labels FS_ventricles
Example 2: get a specific list of list labels
parse_fs_lt_log.py -logfile aparc+aseg_rank.niml.lt.log \
-labels CC_Posterior CC_Mid_Posterior
Example 3: get known plus extra labels
parse_fs_lt_log.py -logfile aparc+aseg_rank.niml.lt.log \
-labels FS_white_matter Left-Cerebellum-Exterior \
-show_all_orig
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terminal options:
-help : show this help
-hist : show the revision history
-ver : show the version number
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process options:
-labels : specify a list of labels to search for
e.g. -labels Left-Cerebral-White-Matter Left-Cerebellum-White-Matter \
Right-Cerebral-White-Matter Right-Cerebellum-White-Matter \
CC_Posterior CC_Mid_Posterior CC_Central CC_Mid_Anterior \
CC_Anterior Brain-Stem
e.g. -labels FS_white_matter
For convenience, there are 2 label groups:
FS_white_matter (as in the example):
Left-Cerebral-White-Matter Left-Cerebellum-White-Matter
Right-Cerebral-White-Matter Right-Cerebellum-White-Matter
CC_Posterior CC_Mid_Posterior CC_Central CC_Mid_Anterior
CC_Anterior Brain-Stem
FS_ventricles
Left-Lateral-Ventricle Left-Inf-Lat-Vent
3rd-Ventricle 4th-Ventricle CSF
Right-Lateral-Ventricle Right-Inf-Lat-Vent 5th-Ventricle
-logfile : specify rank log file
e.g. -logfile aparc+aseg_rank.niml.lt.log
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R Reynolds May, 2016
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