Commit 3f9c609c authored by Alexandre Routier's avatar Alexandre Routier

Update description of -tsv in CLI pipelines

parent 3a65b355
Pipeline #925 passed with stages
in 38 seconds
......@@ -130,8 +130,8 @@ def execute():
from clinica.pipelines.dwi_processing_dti.dwi_processing_dti_cli import DWIProcessingDTICLI # noqa
from clinica.pipelines.fmri_preprocessing.fmri_preprocessing_cli import fMRIPreprocessingCLI # noqa
from clinica.pipelines.pet_volume.pet_volume_cli import PETVolumeCLI # noqa
from clinica.pipelines.statistics_surface.statistics_surface_cli import StatisticsSurfaceCLI # noqa
from clinica.pipelines.pet_surface.pet_surface_cli import PetSurfaceCLI # noqa
from clinica.pipelines.statistics_surface.statistics_surface_cli import StatisticsSurfaceCLI # noqa
pipelines = ClinicaClassLoader(baseclass=CmdParser,
......@@ -149,8 +149,8 @@ def execute():
DWIProcessingDTICLI(),
fMRIPreprocessingCLI(),
PETVolumeCLI(),
PetSurfaceCLI(),
StatisticsSurfaceCLI(),
PetSurfaceCLI()
]
run_parser = sub_parser.add_parser(
......
......@@ -26,7 +26,7 @@ class DWIPreprocessingUsingPhaseDiffFieldmapCLI(ce.CmdParser):
self._args.add_argument("caps_directory",
help='Path to the CAPS directory.')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.') # noqa
help='TSV file containing a list of subjects with their sessions.') # noqa
self._args.add_argument("--low_bval",
type=int, default=5,
......
......@@ -26,7 +26,7 @@ class DWIPreprocessingUsingT1CLI(ce.CmdParser):
self._args.add_argument("caps_directory",
help='Path to the CAPS directory.') # noqa
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.') # noqa
help='TSV file containing a list of subjects with their sessions.') # noqa
self._args.add_argument("--low_bval",
type=int, default=5,
......
......@@ -30,13 +30,10 @@ class DWIProcessingDTICLI(ce.CmdParser):
# Clinica standard arguments (e.g. --n_procs)
clinica_opt = self._args.add_argument_group(PIPELINE_CATEGORIES['CLINICA_OPTIONAL'])
clinica_opt.add_argument("-tsv", "--subjects_sessions_tsv",
metavar=('participants.tsv'),
help='TSV file containing the subjects with their sessions.')
help='TSV file containing a list of subjects with their sessions.')
clinica_opt.add_argument("-wd", "--working_directory",
metavar=('Working_Directory'),
help='Temporary directory to store pipelines intermediate results')
clinica_opt.add_argument("-np", "--n_procs",
metavar=('N'),
type=int,
help='Number of cores used to run in parallel')
clinica_opt.add_argument("-sl", "--slurm",
......
"""fMRI Preprocessing - Clinica Command Line Interface.
This file has been generated automatically by the `clinica generate template`
command line tool. See here for more details: https://gitlab.icm-institute.org/aramis/clinica/wikis/docs/InteractingWithClinica.
"""
# coding: utf8
import clinica.engine as ce
......@@ -26,30 +22,30 @@ class fMRIPreprocessingCLI(ce.CmdParser):
"""
self._args.add_argument("bids_directory",
help='Path to the BIDS directory')
help='Path to the BIDS directory.')
self._args.add_argument("caps_directory",
help='Path to the CAPS directory')
help='Path to the CAPS directory.')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions')
help='TSV file containing a list of subjects with their sessions.')
self._args.add_argument("-wd", "--working_directory",
help='Temporary directory to store pipelines intermediate results')
help='Temporary directory to store pipelines intermediate results.')
self._args.add_argument("-np", "--n_procs", type=int,
help='Number of processors to run in parallel')
help='Number of processors to run in parallel.')
self._args.add_argument("-sl", "--slurm", action='store_true',
help='Run the pipelines using SLURM')
help='Run the pipelines using SLURM.')
self._args.add_argument("-sa", "--sbatch_args",
help='SLURM\'s sbatch tool arguments')
help='SLURM\'s sbatch tool arguments.')
self._args.add_argument("-fwhm", "--full_width_at_half_maximum",
nargs=3, type=int, default=[8, 8, 8],
help="Size of the fwhm filter in milimeters to smooth the image")
help="Size of the fwhm filter in milimeters to smooth the image.")
self._args.add_argument("-t1s", "--t1_native_space", action='store_true',
help="Also return images in T1 native space")
help="Also return images in T1 native space.")
self._args.add_argument("-fsbm", "--freesurfer_brain_mask",
action='store_true',
help="Use Freesurfer's pre-computed brain mask")
help="Use FreeSurfer's pre-computed brain mask.")
self._args.add_argument("-u", "--unwarping",
action='store_true',
help="Add SPM's Unwarping to the Realign step")
help="Add SPM's Unwarping to the Realign step.")
def run_command(self, args):
......
......@@ -23,7 +23,7 @@ class PetSurfaceCLI(ce.CmdParser):
def define_description(self):
"""Define a description of this pipeline.
"""
self._description = 'Surface-based processing of PET images:\nhttps://gitlab.icm-institute.org/aramislab/clinica-aramis/wikis/docs/Pipelines/PET_CorticalProjection'
self._description = 'Surface-based processing of PET images:\nhttp://clinica.run/doc/Pipelines/PET_Surface/'
def define_options(self):
"""Define the sub-command arguments
......@@ -32,9 +32,9 @@ class PetSurfaceCLI(ce.CmdParser):
self._args.add_argument("bids_directory",
help='Path to the BIDS directory.')
self._args.add_argument("caps_directory",
help='Path to the CAPS directory. (Filled with results from t1-freesurfer')
help='Path to the CAPS directory. (Filled with results from t1-freesurfer-cross-sectional')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.')
help='TSV file containing a list of subjects with their sessions.')
self._args.add_argument("-pt", "--pet_tracer", type=str, default='fdg',
help='PET tracer type. Can be fdg or av45. Default value : fdg')
self._args.add_argument("-wd", "--working_directory",
......
......@@ -22,7 +22,7 @@ class PETVolumeCLI(ce.CmdParser):
def define_description(self):
"""Define a description of this pipeline.
"""
self._description = 'SPM-based pre-processing of PET images:\nhttp://clinica.run/doc/Pipelines/PET_Preprocessing/'
self._description = 'SPM-based pre-processing of PET images:\nhttp://clinica.run/doc/Pipelines/PET_Volume/'
def define_options(self):
"""Define the sub-command arguments
......
......@@ -33,7 +33,7 @@ class T1FreeSurferCrossSectionalCLI(ce.CmdParser):
self._args.add_argument("caps_directory",
help='Path to the CAPS directory.')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.')
help='TSV file containing a list of subjects with their sessions.')
# Custom args added by developers
self._args.add_argument("-ras", "--recon_all_args",
help='additional flags for recon-all command line, default will be -qcache')
......
# coding: utf8
"""T1 SPM Dartel - Clinica Command Line Interface.
This file has been generated automatically by the `clinica generate template`
command line tool. See here for more details: https://gitlab.icm-institute.org/aramis/clinica/wikis/docs/InteractingWithClinica.
"""
import clinica.engine as ce
__author__ = "Jorge Samper Gonzalez"
......@@ -28,7 +22,7 @@ class T1VolumeCreateDartelCLI(ce.CmdParser):
def define_description(self):
"""Define a description of this pipeline.
"""
self._description = 'DARTEL creation with SPM:\nhttp://clinica.run/doc/Pipelines/T1_SPM_Full/'
self._description = 'DARTEL creation with SPM:\nhttp://clinica.run/doc/Pipelines/T1_Volume/'
def define_options(self):
"""Define the sub-command arguments
......@@ -40,7 +34,7 @@ class T1VolumeCreateDartelCLI(ce.CmdParser):
self._args.add_argument("group_id",
help='Current group name')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.')
help='TSV file containing a list of subjects with their sessions.')
self._args.add_argument("-dt", "--dartel_tissues", nargs='+', type=int, default=[1, 2, 3], choices=range(1, 7),
help='Tissues to use for DARTEL template calculation. Ex: 1 is only GM')
self._args.add_argument("-wd", "--working_directory",
......
# coding: utf8
"""T1 SPM Dartel2MNI - Clinica Command Line Interface.
This file has been generated automatically by the `clinica generate template`
command line tool. See here for more details: https://gitlab.icm-institute.org/aramis/clinica/wikis/docs/InteractingWithClinica.
"""
import clinica.engine as ce
__author__ = "Jorge Samper Gonzalez"
......@@ -28,7 +22,7 @@ class T1VolumeDartel2MNICLI(ce.CmdParser):
def define_description(self):
"""Define a description of this pipeline.
"""
self._description = 'Register DARTEL template to MNI space with SPM:\nhttp://clinica.run/doc/Pipelines/T1_SPM_Full/'
self._description = 'Register DARTEL template to MNI space with SPM:\nhttp://clinica.run/doc/Pipelines/T1_Volume/'
def define_options(self):
"""Define the sub-command arguments
......@@ -41,7 +35,7 @@ class T1VolumeDartel2MNICLI(ce.CmdParser):
self._args.add_argument("group_id",
help='Current group name')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.')
help='TSV file containing a list of subjects with their sessions.')
self._args.add_argument("-t", "--tissues", nargs='+', type=int, default=[1, 2, 3], choices=range(1, 7),
help='Tissues to register into MNI space. Ex: 1 is only GM')
self._args.add_argument("-fwhm", "--fwhm", nargs='+', type=int, default=[8],
......
# coding: utf8
"""T1 SPM Dartel Existing Template - Clinica Command Line Interface.
This file has been generated automatically by the `clinica generate template`
command line tool. See here for more details: https://gitlab.icm-institute.org/aramislab/clinica/wikis/docs/InteractingWithClinica.
"""
import clinica.engine as ce
__author__ = "Jorge Samper Gonzalez"
......@@ -27,7 +21,7 @@ class T1VolumeExistingTemplateCLI(ce.CmdParser):
def define_description(self):
"""Define a description of this pipeline.
"""
self._description = 'Create new DARTEL template based on a current DARTEL template:\nhttp://clinica.run/doc/Pipelines/T1_SPM_Full/'
self._description = 'Create new DARTEL template based on a current DARTEL template:\nhttp://clinica.run/doc/Pipelines/T1_Volume/'
def define_options(self):
"""Define the sub-command arguments
......@@ -39,7 +33,7 @@ class T1VolumeExistingTemplateCLI(ce.CmdParser):
self._args.add_argument("group_id",
help='Current group name')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.')
help='TSV file containing a list of subjects with their sessions.')
self._args.add_argument("-t", "--tissues", nargs='+', type=int, default=[1, 2, 3], choices=range(1, 7),
help='Tissues to create flow fields to DARTEL template. Ex: 1 is only GM')
self._args.add_argument("-wd", "--working_directory",
......
# coding: utf8
"""T1 SPM Full Prep - Clinica Command Line Interface.
This file has been generated automatically by the `clinica generate template`
command line tool. See here for more details: https://gitlab.icm-institute.org/aramislab/clinica/wikis/docs/InteractingWithClinica.
"""
import clinica.engine as ce
__author__ = "Jorge Samper Gonzalez"
......@@ -28,7 +22,7 @@ class T1VolumeNewTemplateCLI(ce.CmdParser):
def define_description(self):
"""Define a description of this pipeline.
"""
self._description = 'SPM-based pre-processing of T1w images:\nhttp://clinica.run/doc/Pipelines/T1_SPM_Full/'
self._description = 'SPM-based pre-processing of T1w images:\nhttp://clinica.run/doc/Pipelines/T1_Volume/'
def define_options(self):
"""Define the sub-command arguments
......@@ -51,7 +45,7 @@ class T1VolumeNewTemplateCLI(ce.CmdParser):
clinica_opt = self._args.add_argument_group(PIPELINE_CATEGORIES['CLINICA_OPTIONAL'])
clinica_opt.add_argument("-tsv", "--subjects_sessions_tsv",
metavar=('participants.tsv'),
help='TSV file containing the subjects with their sessions.')
help='TSV file containing a list of subjects with their sessions.')
clinica_opt.add_argument("-wd", "--working_directory",
metavar=('Working_Directory'),
help='Temporary directory to store pipelines intermediate results')
......
# coding: utf8
"""spm_parcellation - Clinica Command Line Interface.
This file has been generated automatically by the `clinica generate template`
command line tool. See here for more details:
https://gitlab.icm-institute.org/aramislab/clinica/wikis/docs/InteractingWithClinica.
"""
__author__ = "Simona Bottani"
__copyright__ = "Copyright 2016-2018, The Aramis Lab Team"
__credits__ = ["Simona Bottani"]
......@@ -24,9 +16,13 @@ class T1VolumeParcellationCLI(ce.CmdParser):
def define_name(self):
"""Define the sub-command name to run this pipeline.
"""
self._name = 't1-volume-parcellation'
def define_description(self):
"""Define a description of this pipeline.
"""
self._description = 'Computation of mean GM concentration for a set of regions:\nhttp://clinica.run/doc/Pipelines/T1_Volume/'
def define_options(self):
"""Define the sub-command arguments
"""
......@@ -38,7 +34,7 @@ class T1VolumeParcellationCLI(ce.CmdParser):
self._args.add_argument("group_id",
help = 'Current group name')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.')
help='TSV file containing a list of subjects with their sessions.')
#self._args.add_argument("-im_type", "--image_type", type = str, default = 'T1',
# choices =['T1', 'pet'],
# help = 'image type. Possible values are T1 and pet')
......
# coding: utf8
"""T1 SPM Segmentation - Clinica Command Line Interface.
This file has been generated automatically by the `clinica generate template`
command line tool. See here for more details: https://gitlab.icm-institute.org/aramis/clinica/wikis/docs/InteractingWithClinica.
"""
import clinica.engine as ce
__author__ = "Jorge Samper Gonzalez"
......@@ -28,7 +22,7 @@ class T1VolumeTissueSegmentationCLI(ce.CmdParser):
def define_description(self):
"""Define a description of this pipeline.
"""
self._description = 'Tissue segmentation of T1w images with SPM:\nhttp://clinica.run/doc/Pipelines/T1_SPM_Full/'
self._description = 'Tissue segmentation, bias correction and spatial normalization to MNI space of T1w images with SPM:\nhttp://clinica.run/doc/Pipelines/T1_Volume/'
def define_options(self):
"""Define the sub-command arguments
......@@ -38,7 +32,7 @@ class T1VolumeTissueSegmentationCLI(ce.CmdParser):
self._args.add_argument("caps_directory",
help='Path to the CAPS directory.')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.')
help='TSV file containing a list of subjects with their sessions.')
self._args.add_argument("-ti", "--tissue_classes", nargs='+', type=int, default=[1, 2, 3], choices=range(1, 7),
help="Tissue classes (gray matter, GM; white matter, WM; cerebro-spinal fluid, CSF...) to save. Up to 6 tissue classes can be saved. Ex: 1 2 3 is GM, WM and CSF")
self._args.add_argument("-dt", "--dartel_tissues", nargs='+', type=int, default=[1, 2, 3], choices=range(1, 7),
......
......@@ -27,7 +27,7 @@ class {{ pipeline.class_name }}CLI(ce.CmdParser):
# self._args.add_argument("caps_directory",
# help='Path to the CAPS directory.')
# self._args.add_argument("-tsv", "--subjects_sessions_tsv",
# help='TSV file containing the subjects with their sessions.')
# help='TSV file containing a list of subjects with their sessions.')
# Add your own pipeline command line arguments here to be used in the
# method below. Example below:
self._args.add_argument("-hw", "--hello_word_arg",
......
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