def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('output_report',
help='Filename of QC report (in html format).')
p.add_argument('--bval',
nargs='+',
required=True,
help='List of bval files.')
p.add_argument('--bvec',
nargs='+',
required=True,
help='List of bvec files.')
p.add_argument('--tolerance',
'-t',
metavar='INT',
type=int,
default=20,
help='The tolerated gap between the b-values to '
'extract\nand the actual b-values.')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('output_report',
help='HTML report')
p.add_argument('lut',
help='Look Up Table for RGB')
p.add_argument('--t1', nargs='+', required=True,
help='T1 images in Nifti format')
p.add_argument('--label', nargs='+', required=True,
help='Label images in Nifti format')
p.add_argument('--skip', default=2, type=int,
help='Number of images skipped to build the mosaic. [%(default)s]')
p.add_argument('--nb_columns', default=12, type=int,
help='Number of columns for the mosaic. [%(default)s]')
p.add_argument('--nb_threads', type=int, default=1,
help='Number of threads. [%(default)s]')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('frf', nargs='+',
help='Fiber response function (frf) files (in txt format).')
p.add_argument('output_report',
help='Filename of QC report (in html format).')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('output_report', help='HTML report')
p.add_argument('--t1_warped',
nargs='+',
required=True,
help='T1 registered images in Nifti format')
p.add_argument('--rgb',
nargs='+',
required=True,
help='RGB images in Nifti format')
p.add_argument('--wm',
nargs='+',
required=True,
help='WM mask in Nifti format')
p.add_argument('--gm',
nargs='+',
required=True,
help='GM mask in Nifti format')
p.add_argument('--csf',
nargs='+',
required=True,
help='CSF mask in Nifti format')
p.add_argument(
'--skip',
default=2,
type=int,
help='Number of images skipped to build the mosaic. [%(default)s]')
p.add_argument('--nb_columns',
default=12,
type=int,
help='Number of columns for the mosaic. [%(default)s]')
p.add_argument('--nb_threads',
type=int,
default=1,
help='Number of threads. [%(default)s]')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('output_report', help='HTML report')
p.add_argument('data', nargs='+', help='Screenshot folders')
p.add_argument('--sym_link',
action="store_true",
help='Use symlink instead of copy')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('output_report',
help='HTML report')
p.add_argument('--tractograms', nargs='+',
help='Tractograms in format supported by Nibabel')
p.add_argument('--t1', nargs='+',
help='T1 images in Nifti format')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('tracking_type',
choices=["pft", "local"],
help='Tracking type')
p.add_argument('output_report', help='HTML report')
p.add_argument('--seeding_mask',
nargs='+',
required=True,
help='Seeding mask in Nifti format')
p.add_argument('--tracking_mask',
nargs='+',
help='Tracking mask in Nifti format')
p.add_argument('--map_include',
nargs='+',
help='Map include in Nifti format')
p.add_argument('--map_exclude',
nargs='+',
help='Map exlude in Nifti format')
p.add_argument(
'--skip',
default=2,
type=int,
help='Number of images skipped to build the mosaic. [%(default)s]')
p.add_argument('--nb_columns',
default=12,
type=int,
help='Number of columns for the mosaic. [%(default)s]')
p.add_argument('--nb_threads',
type=int,
default=1,
help='Number of threads. [%(default)s]')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('output_report',
help='HTML report')
p.add_argument('--fa', nargs='+', required=True,
help='FA images in Nifti format')
p.add_argument('--md', nargs='+', required=True,
help='MD images in Nifti format')
p.add_argument('--rd', nargs='+', required=True,
help='RD images in Nifti format')
p.add_argument('--ad', nargs='+', required=True,
help='AD images in Nifti format')
p.add_argument('--residual', nargs='+', required=True,
help='Residual images in Nifti format')
p.add_argument('--evecs_v1', nargs='+', required=True,
help='Evecs v1 images in Nifti format')
p.add_argument('--wm', nargs='+', required=True,
help='WM mask in Nifti format')
p.add_argument('--gm', nargs='+', required=True,
help='GM mask in Nifti format')
p.add_argument('--csf', nargs='+', required=True,
help='CSF mask in Nifti format')
p.add_argument('--skip', default=2, type=int,
help='Number of images skipped to build the mosaic. [%(default)s]')
p.add_argument('--nb_columns', default=12, type=int,
help='Number of columns for the mosaic. [%(default)s]')
p.add_argument('--nb_threads', type=int, default=1,
help='Number of threads. [%(default)s]')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('image_type', help='Type of image (e.g. B0 resample)')
p.add_argument('output_report', help='HTML report')
p.add_argument('--images',
nargs='+',
required=True,
help='Images in Nifti format')
p.add_argument('--wm', nargs='+', help='WM mask in Nifti format')
p.add_argument('--gm', nargs='+', help='GM mask in Nifti format')
p.add_argument('--csf', nargs='+', help='CSF mask in Nifti format')
p.add_argument(
'--skip',
default=2,
type=int,
help='Number of images skipped to build the mosaic. [%(default)s]')
p.add_argument('--nb_columns',
default=12,
type=int,
help='Number of columns for the mosaic. [%(default)s]')
p.add_argument(
'--duration',
default=100,
type=int,
help='Duration of each image in GIF in milliseconds [%(default)s]')
p.add_argument('--nb_threads',
type=int,
default=1,
help='Number of threads. [%(default)s]')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('image_type', help='Type of image (e.g. B0).')
p.add_argument('output_report',
help='Filename of QC report (in html format).')
p.add_argument('--images_no_bet',
nargs='+',
required=True,
help='List of images with the skull in Nifti format.')
p.add_argument('--images_bet_mask',
nargs='+',
required=True,
help='List of brain extraction masks in Nifti format.')
p.add_argument(
'--skip',
default=2,
type=int,
help='Number of images skipped to build the mosaic. [%(default)s]')
p.add_argument('--nb_columns',
default=12,
type=int,
help='Number of columns for the mosaic. [%(default)s]')
p.add_argument('--nb_threads',
type=int,
default=1,
help='Number of threads. [%(default)s]')
add_overwrite_arg(p)
return p
