3 md@sDddlZddlmZddlmZddlmZddlmZddZdS)N)glob)split_filename)dedent)RawDescriptionHelpFormatterc Cstd}dtjjkr>ttjjtjdd}dd|D}ng}|jddd}||_t |_ |j dd d d|j d d d d|j ddd|dd|j dddddd|j dddddddddgd d!|j d"d#d$t d%d&|j d'd(d)d|j d*d+d,d-|S).Na Process subject-level data in fitz. This script controls the workflows that process data. Depending on the workflow, the data may start from raw DICOM or Nifti files and finish as processed models or group-level stats. See the documentation for the pipeline (collection of workflows) for information on exactly what the image inputs and outputs will be. All fitz workflows use Nipype, so there are several common options for efficiently running multiple subjects at once with differnt nipype plugins. The script can thus be run for several subjects at once, and (with a large enough cluster) all of the subjects can be processed in the time it takes to process a single run of data linearly. Nipype creates a cache directory to save processing time when steps are re-run. If you do not delete your cache directory after running (which is configured in the project file), repeated use of this script will only rerun the nodes that have changes to their inputs. Otherwise, you will have to rerun at the level of the workflows. Examples -------- Note that the parameter switches match any unique short version of the full parameter name. fitz run -w xnatconvert preproc onset model Run every stage of the standar SPM fMRI pipeline for the default experiment for each subject defined in $FITZ_DIR/subjects.txt. The processing will be distributed locally with the MultiProc plugin using 4 processes. fitz run -s subj1 subj2 subj3 -w preproc Run preprocessing of the default experiment for subjects `subj1`, `subj2`, and `subj3`. fitz run -s pilot_subjects -w model -e nback -n 8 Run the model workflow on the subjects enumerated in $FITZ_DIR/pilot_subjects.txt with the experiment details in $FITZ_DIR/nback.py. Distribute the execution locally with 8 parallel processes. Usage Details ------------- ZFITZ_DIRz*/workflows/*.pycSsg|]}t|dqS))r).0Zwfr6/tmp/pip-build-7vycvbft/fitz/fitz/tools/commandline.py @szrun_parser..run)helpz --experimentz-ezexperimental paradigmz--modelz-mz model to fitz --workflowsz-w*zwhich workflows to run)nargschoicesr z --subjectsz-sZsubjectsz`list of subject ids, name of file in lyman directory, or full path to text file with subject ids)rdestr z--pluginz-pZ multiprocZlinearZipythonZtorqueZsgeZslurmzworklow execution plugin)defaultrr z--nprocsz-nz$number of MultiProc processes to use)rtyper z--queuez-qz#which queue for scheduler executionz --dontrun store_truez$don't actually execute the workflows)actionr ) rosenvironkeysrpathjoinZ add_parser descriptionrZformatter_class add_argumentint)Z subparsersr Zwf_filesZ workflowsparserrrr run_parsers43     r) rrZnipype.utils.filemaniprtextwraprargparserrrrrr s