add scripts for Fastsurfer orchestration on slurm clusters #388
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fix python-s in run_fastsurfer.sh (only use this if it is defined, else use python3.10 -- this is the default value and the in-docker fix to ignore user-space packages) fix bashrc definition in Docker/Dockerfile
rewrite/update N4_bias_correct.py - accept additional parameters (--aseg, --verbosity, --version) - port from optparse to argparse - change printing to logging facilities (instead of print), verbosity changes amount of prints. - rename functions and variables to follow PEP8 (lowercase, underscore to separate) - add function and integration to process the aseg and calculate wm intensity based on the wm segmentation from aseg - change normalization code to keep the zero-base (robust scaling should be done previously, e.g. typically in conforming) - rearrange code structure so functions are not as dependent on flags. Specifically, whether or not specific flags/files are present is moved to the main script. Consequently, functions are more predictable and not dependent on arguments.
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Nice! I wonder if it makes sense to move these into a slurm subdirectory or into the singularity subdir? |
m-reuter
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m-reuter
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fix doc string talairach origin
change the renormalization (--skipwm mode) to only consider the average intensity of the masked image. fix docstring in image_io.py
- minimal reorder and formatting add - brun_fastsurfer.sh: a batch version of run_fastsurfer.sh - srun_fastsurfer.sh: a slurm/orchestration script for run_fastsurfer.sh (and brun_fastsurfer.sh) - stool.sh: functions for srun_* and brun_*
add statusfile and do not fail in brun_fastsurfer.sh so a single segmentation failed does not break the pipeline fix double prepend in_dir in check_subject_images cleanup the job dependencies of seg, surf and cleanup
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fix wait in brun_fastsurfer add Note/Error message for invalid path to t1 in run_fastsurfer.sh update srun_fastsurfer docs: - usage: output folder structure - check of out_dir - update of statusfile add --no-home for singularity fix copyjob for --surf_only (srun_fastsurfer) add time (timelimit) fix check_seg_surf_only() move out_folders into a slurm folder fix $dir in cleanup fix copy script
no jobstep in segmentation fix premature creation of the hpc_work directory create hpc_work dir on demand make cleanup script only delete the folder if all the moving was successful
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Includes the bias field commits
Adds three files to run Fastsurfer on a subject_list file and on a slurm cluster in a resource-optimized way.
Known issues:
On our slurm cluster I experienced some sporadic out-of-memory issues where they should not have happened. These need to be investigated.