Add brainvol stats to the segstats command #474
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dkuegler
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Apr 21, 2024
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- develop Measures in header mri_segstats.py - add mri_segstats wrapper script utils.py - add LTADict TypedDict - rename readLT to read_lta - clean up read_lta function parser_defaults.py - make FASTSURFER_ROOT a Path object pyproject.toml - update version run_tools.py - formatting data_utils.py - make read_classes_from_lut accept and work with Path objects
…ion elements) fix the results of mri_brainvol_stats.py to be identical to mri_brainvol_stats merge read_classes_from_lut from segstats and data_utils fix sorting of measures in mri_brainvol_stats.py (make default_measures a variable instead of a constant) fix classes for CorpusCallosum and BrainSeg remove superfluous cases and classes
Fix measures --import <measures> settings Add measures to aseg+DKT.stats file Better error message if trying to import a measure that does not exist Remove default values for imported measures (name, description and unit are read from the file anyways) Add DKT regions to BrainVol Measure remove brainvol_statsfile parameter and internal references, brainvolstats are now either saved into segstats files, or if no pvfile or normfile is passed there is just a brainvol.stats-like file generated (in legacy_freesurfer mode, plus a message written to the console) Fix default value for volume_precision Fix empty function Update call of segstats in run_fastsurfer.sh
…stats/brainvol.stats>.
…nctions.sh. recon_surf/recon-surf.sh - Add a --segstats_legacy flag - Put together consecutive statements that are piped to the same process, group them for less io/handles - Update calls to segstats.py and mri_segstats.py - fix id statements to get the username
- add pv_guide value FastSurferCNN/utils/arg_types.py - Fix docstring and typing FastSurferCNN/utils/brainvolstats.py - move default value for source segmentation file for Measures FastSurferCNN/segstats.py - Fix integration of brainvolstats recon_surf/recon-surf.sh and run_fastsurfer.sh - Integrate brainvolstats
update license checking
better save_maps test
- remove nbsphinx from sphinx extensions
- suppress autosectionlabel warnings in sphinx - fix doc recon-surf - fix the vox-size check - fix which stats are calculated when run_fastsurfer.sh - remove echo_quoted
…I. Order of --import and --compute matters for ordering in the output file. fix mri_segstats.py for the unification of computed_measures and imported_measures
- Fix/clean up Manager.__init__: parameters associated with segmentation map passing - Fix errors of storage/caching of measures FastSurferCNN/mri_brainvol_stats.py - Fix API to Manager.__init__ -> measures should be (is_imported, measure_string) instead of only measure_string split into computed_measures and imported_measures FastSurferCNN/mri_segstats.py - Adapt script to new Manager.__init__ interface -> measures should be (is_imported, measure_string) instead of only measure_string split into computed_measures and imported_measures FastSurferCNN/segstats.py - Adapt script to new Manager.__init__ interface -> measures should be (is_imported, measure_string) instead of only measure_string split into computed_measures and imported_measures
- Fix Manager.format_measures to have use the same ordering of measures are the order in the arguments (all always last) - Fix the spelling of the BrainSegVolNotSurf Measure - Add Manager.needs_pv_calculation function to indicate when the Manager needs PV values FastSurferCNN/mri_brainvol_stats.py - Add measure_only=True - Add --pvfile argument, so --no_legacy is actually possible. - Use segstats.py main function instead of its own and remove this main function. FastSurferCNN/mri_segstats.py - Adapt script to new Manager.__init__ interface -> measures should be (is_imported, measure_string) instead of only measure_string split into computed_measures and imported_measures FastSurferCNN/segstats.py - Add --measure_only flag for brainvol.stats-like output - Fix and optimize brainvol.stats output recon_surf/recon-surf.sh - Some cleanup (e.g. send pushd/popd output to /dev/null) - Fix the parameters of the segstats-py calls
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Fix formatting
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m-reuter
reviewed
Aug 21, 2024
This PR adds all the brainvol stats measures to segstats.py. This specifically includes eTIV and summary volumes.
It also adds
mri_segstats.pyandmri_brainvol_stats.py, which mimic freesurfer binaries, based on this code. They are much faster and use similar command line APIs (as compared to segstats.py, which has a different API).