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Copy file name to clipboardExpand all lines: bidscoin/cli/_bidscoiner.py
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parser.add_argument('-b','--bidsmap', help='The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the basename (i.e. no "/" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml', default='bidsmap.yaml')
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parser.add_argument('-f','--force', help='Process all subjects, regardless of existing subject folders in the bidsfolder. Otherwise these subject folders will be skipped', action='store_true')
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parser.add_argument('-c','--cluster', help='Use the DRMAA library to submit the bidscoiner jobs to a high-performance compute (HPC) cluster', action='store_true')
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parser.add_argument('-n','--nativespec', help='Opaque DRMAA argument with native specifications for submitting bidscoiner jobs to the HPC cluster. NB: Use quotes and include at least one space character to prevent overearly parsing (default: -l walltime=00:30:00,mem=4gb)', default='-l walltime=00:30:00,mem=4gb')
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parser.add_argument('-n','--nativespec', help='Opaque DRMAA argument with native specifications for submitting bidscoiner jobs to the HPC cluster. NB: Use quotes and include at least one space character to prevent premature parsing (default: -l walltime=00:30:00,mem=4gb)', default='-l walltime=00:30:00,mem=4gb')
Copy file name to clipboardExpand all lines: bidscoin/cli/_deface.py
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@@ -34,7 +34,7 @@ class CustomFormatter(argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescri
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parser.add_argument('-p','--participant_label', help='Space separated list of sub-# identifiers to be processed (the sub-prefix can be left out). If not specified then all sub-folders in the bidsfolder will be processed', nargs='+')
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parser.add_argument('-o','--output', help=f"A string that determines where the defaced images are saved. It can be the name of a BIDS datatype folder, such as 'anat', or of the derivatives folder, i.e. 'derivatives'. If output is left empty then the original images are replaced by the defaced images")
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parser.add_argument('-c','--cluster', help='Use the DRMAA library to submit the deface jobs to a high-performance compute (HPC) cluster', action='store_true')
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parser.add_argument('-n','--nativespec', help='Opaque DRMAA argument with native specifications for submitting deface jobs to the HPC cluster (NB: Use quotes and include at least one space character to prevent overearly parsing)', default='-l walltime=00:30:00,mem=2gb')
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parser.add_argument('-n','--nativespec', help='Opaque DRMAA argument with native specifications for submitting deface jobs to the HPC cluster (NB: Use quotes and include at least one space character to prevent premature parsing)', default='-l walltime=00:30:00,mem=2gb')
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parser.add_argument('-a','--args', help='Additional arguments (in dict/json-style) that are passed to pydeface (NB: Use quotes). See examples for usage', type=json.loads, default={})
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parser.add_argument('-f','--force', help='Deface all images, regardless if they have already been defaced (i.e. if {"Defaced": True} in the json sidecar file)', action='store_true')
Copy file name to clipboardExpand all lines: bidscoin/cli/_medeface.py
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@@ -37,7 +37,7 @@ class CustomFormatter(argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescri
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parser.add_argument('-p','--participant_label', help='Space separated list of sub-# identifiers to be processed (the sub-prefix can be left out). If not specified then all sub-folders in the bidsfolder will be processed', nargs='+')
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parser.add_argument('-o','--output', help=f"A string that determines where the defaced images are saved. It can be the name of a BIDS datatype folder, such as 'anat', or of the derivatives folder, i.e. 'derivatives'. If output is left empty then the original images are replaced by the defaced images")
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parser.add_argument('-c','--cluster', help='Use the DRMAA library to submit the deface jobs to a high-performance compute (HPC) cluster', action='store_true')
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parser.add_argument('-n','--nativespec', help='Opaque DRMAA argument with native specifications for submitting deface jobs to the HPC cluster (NB: Use quotes and include at least one space character to prevent overearly parsing)', default='-l walltime=00:30:00,mem=2gb')
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parser.add_argument('-n','--nativespec', help='Opaque DRMAA argument with native specifications for submitting deface jobs to the HPC cluster (NB: Use quotes and include at least one space character to prevent premature parsing)', default='-l walltime=00:30:00,mem=2gb')
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parser.add_argument('-a','--args', help='Additional arguments (in dict/json-style) that are passed to pydeface (NB: Use quotes). See examples for usage', type=json.loads, default={})
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parser.add_argument('-f','--force', help='Process all images, regardless if images have already been defaced (i.e. if {"Defaced": True} in the json sidecar file)', action='store_true')
Copy file name to clipboardExpand all lines: bidscoin/cli/_skullstrip.py
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parser.add_argument('-m','--masked', help="Globlike search pattern (relative to the subject/session folder) to select additional (3D/4D) images from the same space that need to be masked with the same mask, e.g. 'fmap/*_phasediff'. NB: This option can only be used if pattern yields a single file per session", type=str)
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parser.add_argument('-o','--output', help="One or two output strings that determine where the skullstripped + additional masked images are saved. Each output string can be the name of a BIDS datatype folder, such as 'anat', or of the derivatives folder, i.e. 'derivatives' (default). If the output string is the same as the datatype then the original images are replaced by the skullstripped images", nargs='+')
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parser.add_argument('-f','--force', help="Process images, regardless whether images have already been skullstripped (i.e. if {'SkullStripped': True} in the json sidecar file)", action='store_true')
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parser.add_argument('-a','--args', help="Additional arguments that are passed to synthstrip (NB: Use quotes and include at least one space character to prevent overearly parsing)", type=str, default='')
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parser.add_argument('-a','--args', help="Additional arguments that are passed to synthstrip (NB: Use quotes and include at least one space character to prevent premature parsing)", type=str, default='')
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parser.add_argument('-c','--cluster', help='Use the DRMAA library to submit the skullstrip jobs to a high-performance compute (HPC) cluster', action='store_true')
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parser.add_argument('-n','--nativespec', help='Opaque DRMAA argument with native specifications for submitting skullstrip jobs to the HPC cluster (NB: Use quotes and include at least one space character to prevent overearly parsing)', default='-l walltime=0:05:00,mem=8gb')
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parser.add_argument('-n','--nativespec', help='Opaque DRMAA argument with native specifications for submitting skullstrip jobs to the HPC cluster (NB: Use quotes and include at least one space character to prevent premature parsing)', default='-l walltime=0:05:00,mem=8gb')
Copy file name to clipboardExpand all lines: bidscoin/cli/_slicereport.py
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parser.add_argument('-q','--qcscores', help="Column names for creating an accompanying tsv-file to store QC-rating scores (default: rating_overall)", default=['rating_overall'], nargs='+')
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parser.add_argument('-c','--cluster', help='Use `torque` or `slurm` to submit the slicereport jobs to a high-performance compute (HPC) cluster', choices=['torque','slurm'])
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parser.add_argument('-m','--mem', help='The amount of requested memory in GB for the cluster jobs', default='')
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parser.add_argument('--operations', help='One or more fslmaths operations that are performed on the input image (before slicing it for the report). OPERATIONS is opaquely passed as is: `fslmaths inputimage OPERATIONS reportimage`. NB: Use quotes and include at least one space character to prevent overearly parsing, e.g. " -Tmean" or "-Tstd -s 3" (default: -Tmean)', default='-Tmean')
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parser.add_argument('--operations', help='One or more fslmaths operations that are performed on the input image (before slicing it for the report). OPERATIONS is opaquely passed as is: `fslmaths inputimage OPERATIONS reportimage`. NB: Use quotes and include at least one space character to prevent premature parsing, e.g. " -Tmean" or "-Tstd -s 3" (default: -Tmean)', default='-Tmean')
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parser.add_argument('--suboperations', help='The same as OPERATIONS but then for the sub-report instead of the main report: `fslmaths inputimage SUBOPERATIONS subreportimage` (default: -Tmean)', default='-Tmean')
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parser.add_argument('--options', help='Main options of slicer (see below). (default: "s 1")', default=['s','1'], nargs='+')
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parser.add_argument('--outputs', help='Output options of slicer (see below). (default: "x 0.4 x 0.5 x 0.6 y 0.4 y 0.5 y 0.6 z 0.4 z 0.5 z 0.6")', default=['x','0.4','x','0.5','x','0.6','y','0.4','y','0.5','y','0.6','z','0.4','z','0.5','z','0.6'], nargs='+')
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