Usage¶
usage: PipelineQC [-h] {qcpages,combine,image,findfiles,index} ...
qcpages¶
usage: PipelineQC qcpages [-h] [--nipype_plugin NIPYPE_PLUGIN]
[--working_directory WORKING_DIRECTORY]
[--validate_bids] [--exclude EXCLUDE]
[--filter_key FILTER_KEY] [--files FILES]
[--no_index]
config_file output_dir search_dirs [search_dirs ...]
Positional Arguments¶
| config_file | See the Configuration file section |
| output_dir | Output root for QC pages and index file |
| search_dirs | Search these directories for files |
Named Arguments¶
| --nipype_plugin | |
Passed directly to the nipype workflow run method Default: “MultiProc” | |
| --working_directory | |
| Working directory for nipype workflow (i.e., “base_dir”) | |
| --validate_bids | |
If using bids, whether to validate the bids directories Default: False | |
| --exclude | If a filename matches this pattern (using re.search), ignore it. May be specified multiple times |
| --filter_key | Only make pages for certain values of a key. E.g., –filter_key=subject=1:2:10 will only create qc pages for subjects 1, 2, and 10. |
| --files | JSON file from the running the findfiles subcommand |
| --no_index | Do not create an index file Default: False |
combine¶
usage: PipelineQC combine [-h] output_file input_files [input_files ...]
Positional Arguments¶
| output_file | Output filename for tsv file |
| input_files | Input json files |
image¶
usage: PipelineQC image [-h] [--nslices NSLICES] [--output_type {svg,png}]
[--labelimage LABELIMAGE | --probmap PROBMAP]
output_file image
Positional Arguments¶
| output_file | |
| image | Input image |
Named Arguments¶
| --nslices | The number of slices to display for each anatomical plane. Default: 7 |
| --output_type | Possible choices: svg, png Output file type Default: “svg” |
| --labelimage | Label image from which to draw contours |
| --probmap | Probability map |
findfiles¶
usage: PipelineQC findfiles [-h] [--validate_bids] [--exclude EXCLUDE]
config_file output_file search_dirs
[search_dirs ...]
Positional Arguments¶
| config_file | See the Configuration file section |
| output_file | Output JSON file |
| search_dirs | Search these directories for files |
Named Arguments¶
| --validate_bids | |
If using bids, whether to validate the bids directories Default: False | |
| --exclude | If a filename matches this pattern (using re.search), ignore it. May be specified multiple times |