Update to match neurodatascience/nipoppy:main #44
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…d refactored FS extractor (nipoppy#188) * moving sample_global_configs.json and tree.json to the nipoppy subdir * fixed import paths after refactor * fixed import paths after refactor * refactored and cleaned up mriqc run script * refactored and cleaned up mriqc run script * Started tracker refactoring to use doughnut * added a catalog function to identify new proc-participants from bagel and doughnut * added a catalog function to identify new proc-participants from bagel and doughnut * added custom (new subjects only) pybids layout (sqldb) generation * fixed sessions loop and incorporated utils.load_status into run_tracker.py * fixed import path errors and incorporated tracker.py for status flags * fixed global var imports and logging levels * updated sample_run_nipoppy to set log-level and prototypical mriqc run with tracker * updated bids_tracker to match proc_pipe tracker schema * minor fixes and comments * fixed Pandas future warning on setting an item of incompatible dtype * fixed another Pandas future warning on setting an item of incompatible dtype * 1) Updated mriqc and fmirpre run scripts to bind complete bids_dir path, 2) added sqldb generation with ignore list for subjects and datatype+acq, 3) updated sample_run_nipoppy.py to show the these two functionalities. * fixed fmriprep pytest * fixed codespell * fixed NM filename pattern * added functionality to custom map participant_id to bids_id * fixed minor codespell errors * fixed errors from previous merge conflict resolution * updated sample_run_nipoppy to run tractoflow, renamed and moved check_dicom_status, and fixed minor bugs and logging in run_tracker * fixed session_id typo and optimized tracker runs * fixed FS utils function * added acq option to all trackers * added acq option to all trackers (fixed merge conflict) * fixed typos and added support for acq tag in mriqc tracker * fixed tractoflow subject dir path issues and added INCOMPLETE status * refactored FS extraction using brainload package * fixed hemisphere naming * fixed aseg extraction * remove version (i.e. v) prefix from run scripts to match trackers * fixed a typo and removed legacy FS extractor script
bcmcpher
approved these changes
Dec 14, 2023
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PR created/updated automatically by create-pull-request GitHub action. Will be merged automatically by automerge-action if there are no merge conflicts.