Commit e36bc725 authored by Alexandre Routier's avatar Alexandre Routier

Update description of group_id argument in CLI pipelines

parent 3f9c609c
Pipeline #927 passed with stages
in 39 seconds
# fMRI Preprocessing
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# pet_cortical_projection
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......@@ -28,7 +28,6 @@ class PetSurfaceCLI(ce.CmdParser):
def define_options(self):
"""Define the sub-command arguments
"""
self._args.add_argument("bids_directory",
help='Path to the BIDS directory.')
self._args.add_argument("caps_directory",
......
# coding: utf-8
__author__ = "Arnaud Marcoux"
__copyright__ = "Copyright 2016-2018 The Aramis Lab Team"
__credits__ = ["Arnaud Marcoux", "Michael Bacci"]
......
......@@ -33,7 +33,7 @@ class PETVolumeCLI(ce.CmdParser):
self._args.add_argument("caps_directory",
help='Path to the CAPS directory.')
self._args.add_argument("group_id",
help='Current group name')
help='User-defined identifier for the provided group of subjects.')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing the subjects with their sessions.')
self._args.add_argument("-fwhm", "--fwhm_tsv",
......
......@@ -37,8 +37,8 @@ class StatisticsSurfaceCLI(ce.CmdParser):
help='A str to define the contrast matrix for GLM, eg, group. Note, when you want to negative correlation, there is a bug for Clinica commandline currently')
self._args.add_argument("str_format",
help='A str to define the format string for the tsv column , eg, %%s %%s %%s %%f')
self._args.add_argument("group_label",
help='A str for current group name')
self._args.add_argument("group_id",
help='User-defined identifier for the provided group of subjects.')
self._args.add_argument("glm_type",
help='A str based on glm type for the hypothesis, choose one between group_comparison and correlation')
self._args.add_argument("-ft", "--feature_type", type=str, default=None,
......@@ -64,7 +64,6 @@ class StatisticsSurfaceCLI(ce.CmdParser):
"""
Run the pipelines with defined args
"""
from statistics_surface_pipeline import StatisticsSurface
from statistics_surface_utils import check_inputs
from clinica.utils.stream import cprint
......@@ -125,7 +124,7 @@ class StatisticsSurfaceCLI(ce.CmdParser):
'design_matrix': args.design_matrix,
'contrast': args.contrast,
'str_format': args.str_format,
'group_label': args.group_label,
'group_label': args.group_id,
'glm_type': args.glm_type,
'custom_file': args.custom_file,
'feature_label': args.feature_label,
......
......@@ -32,7 +32,7 @@ class T1VolumeCreateDartelCLI(ce.CmdParser):
self._args.add_argument("caps_directory",
help='Path to the CAPS directory.')
self._args.add_argument("group_id",
help='Current group name')
help='User-defined identifier for the provided group of subjects.')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
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),
......
# coding: utf8
"""T1 SPM Dartel - Clinica Pipeline.
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.pipelines.engine as cpe
__author__ = "Jorge Samper Gonzalez"
......@@ -20,13 +15,6 @@ __status__ = "Development"
class T1VolumeCreateDartel(cpe.Pipeline):
"""T1 SPM Dartel SHORT DESCRIPTION.
Warnings:
- A WARNING.
Todos:
- [x] A FILLED TODO ITEM.
- [ ] AN ON-GOING TODO ITEM.
Args:
input_dir: A BIDS directory.
output_dir: An empty output directory where CAPS structured data will be written.
......
# T1 SPM Dartel2MNI
\ No newline at end of file
......@@ -27,13 +27,12 @@ class T1VolumeDartel2MNICLI(ce.CmdParser):
def define_options(self):
"""Define the sub-command arguments
"""
self._args.add_argument("bids_directory",
help='Path to the BIDS directory.')
self._args.add_argument("caps_directory",
help='Path to the CAPS directory.')
self._args.add_argument("group_id",
help='Current group name')
help='User-defined identifier for the provided group of subjects.')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
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),
......
# `t1-spm-dartel-existing-template`` - <VERY_SHORT_DESCRIPTION>
<SHORT_DESCRIPTION>
#### Contents
- [Dependencies](#dependencies)
- [Running the pipeline (command line)](#running-the-pipeline-command-line)
- [Outputs](#outputs)
- [Visualization of the results](#visualization-of-the-results)
- [Describing this pipeline in your paper](#describing-this-pipeline-in-your-paper)
- [Appendix](#appendix)
## Dependencies
If you installed the docker image of Clinica, nothing is required.
If you only installed the core of Clinica, this pipeline needs the installation of **<software_package>** on your computer. You can find how to install this software on the [installation](docs/BeforeYouInstall) page.
## Running the pipeline (command line)
The pipeline can be run with the following command line:
```
clinica run t1-spm-dartel-existing-template bids_directory caps_directory
```
where:
- `bids_directory` is the input folder containing the dataset in a [BIDS](docs/BIDS) hierarchy
- `caps_directory` is the output folder containing the results in a [CAPS](docs/CAPS) hierarchy
- `<ARG_1>` <ARG_1_DESCRIPTION>
- `<ARG_2>` <ARG_2_DESCRIPTION>
## Outputs
Results are stored in the following folder of the [CAPS hierarchy](docs/CAPS): `subjects/sub-<participant_label>/ses-<session_label>/<some_folder>`.
The main output files are:
- `<source_file>_main_ouput_1`: description main output 1.
- `<source_file>_main_ouput_2`: description main output 2.
The full list of output files can be found in the [ClinicA Processed Structure (CAPS) Specification](https://docs.google.com/document/d/14mjXbqRceHK0fD0BIONniLK713zY7DbQHJEV7kxqsd8/edit#heading=h.f4ddnk971gkn).
## Visualization of the results
After the execution of the pipeline, you can check the outputs of a subject by running the command:
> **Notes:**
>
> _The visualization command is not available for the moment. Please come back later, this section will be updated ASAP._
## Describing this pipeline in your paper
> **Example of paragraph:**
>
>_These results have been obtained using the my-pipeline pipeline of Clinica. More precisely ..._
## Appendix
Further information can be found on [this supplementary page](docs/Pipelines/<My_Pipeline_Appendix>).
\ No newline at end of file
......@@ -31,7 +31,7 @@ class T1VolumeExistingTemplateCLI(ce.CmdParser):
self._args.add_argument("caps_directory",
help='Path to the CAPS directory.')
self._args.add_argument("group_id",
help='Current group name')
help='User-defined identifier for the provided group of subjects.')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
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),
......
# `t1-spm-full-prep`` - <VERY_SHORT_DESCRIPTION>
<SHORT_DESCRIPTION>
#### Contents
- [Dependencies](#dependencies)
- [Running the pipeline (command line)](#running-the-pipeline-command-line)
- [Outputs](#outputs)
- [Visualization of the results](#visualization-of-the-results)
- [Describing this pipeline in your paper](#describing-this-pipeline-in-your-paper)
- [Appendix](#appendix)
## Dependencies
If you installed the docker image of Clinica, nothing is required.
If you only installed the core of Clinica, this pipeline needs the installation of **<software_package>** on your computer. You can find how to install this software on the [installation](docs/BeforeYouInstall) page.
## Running the pipeline (command line)
The pipeline can be run with the following command line:
```
clinica run t1-spm-full-prep bids_directory caps_directory
```
where:
- `bids_directory` is the input folder containing the dataset in a [BIDS](docs/BIDS) hierarchy
- `caps_directory` is the output folder containing the results in a [CAPS](docs/CAPS) hierarchy
- `<ARG_1>` <ARG_1_DESCRIPTION>
- `<ARG_2>` <ARG_2_DESCRIPTION>
## Outputs
Results are stored in the following folder of the [CAPS hierarchy](docs/CAPS): `subjects/sub-<participant_label>/ses-<session_label>/<some_folder>`.
The main output files are:
- `<source_file>_main_ouput_1`: description main output 1.
- `<source_file>_main_ouput_2`: description main output 2.
The full list of output files can be found in the [ClinicA Processed Structure (CAPS) Specification](https://docs.google.com/document/d/14mjXbqRceHK0fD0BIONniLK713zY7DbQHJEV7kxqsd8/edit#heading=h.f4ddnk971gkn).
## Visualization of the results
After the execution of the pipeline, you can check the outputs of a subject by running the command:
> **Notes:**
>
> _The visualization command is not available for the moment. Please come back later, this section will be updated ASAP._
## Describing this pipeline in your paper
> **Example of paragraph:**
>
>_These results have been obtained using the my-pipeline pipeline of Clinica. More precisely ..._
## Appendix
Further information can be found on [this supplementary page](docs/Pipelines/<My_Pipeline_Appendix>).
\ No newline at end of file
......@@ -35,7 +35,7 @@ class T1VolumeNewTemplateCLI(ce.CmdParser):
clinica_comp.add_argument("caps_directory",
help='Path to the CAPS directory.')
clinica_comp.add_argument("group_id",
help='Current group name')
help='User-defined identifier for the provided group of subjects.')
# Optional arguments (e.g. FWHM)
optional = self._args.add_argument_group(PIPELINE_CATEGORIES['OPTIONAL'])
optional.add_argument("-fwhm", "--fwhm",
......
# coding: utf8
"""T1 SPM Full Prep - Clinica Pipeline.
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.pipelines.engine as cpe
__author__ = "Jorge Samper Gonzalez"
......@@ -21,13 +15,6 @@ __status__ = "Development"
class T1VolumeNewTemplate(cpe.Pipeline):
"""T1 SPM Full Prep SHORT DESCRIPTION.
Warnings:
- A WARNING.
Todos:
- [x] A FILLED TODO ITEM.
- [ ] AN ON-GOING TODO ITEM.
Args:
input_dir: A BIDS directory.
output_dir: An empty output directory where CAPS structured data will be written.
......
# `spm_parcellation`` - <VERY_SHORT_DESCRIPTION>
<SHORT_DESCRIPTION>
#### Contents
- [Dependencies](#dependencies)
- [Running the pipeline (command line)](#running-the-pipeline-command-line)
- [Outputs](#outputs)
- [Visualization of the results](#visualization-of-the-results)
- [Describing this pipeline in your paper](#describing-this-pipeline-in-your-paper)
- [Appendix](#appendix)
## Dependencies
If you installed the docker image of Clinica, nothing is required.
If you only installed the core of Clinica, this pipeline needs the installation of **<software_package>** on your computer. You can find how to install this software on the [installation](docs/BeforeYouInstall) page.
## Running the pipeline (command line)
The pipeline can be run with the following command line:
```
clinica run spm_parcellation bids_directory caps_directory
```
where:
- `bids_directory` is the input folder containing the dataset in a [BIDS](docs/BIDS) hierarchy
- `caps_directory` is the output folder containing the results in a [CAPS](docs/CAPS) hierarchy
- `<ARG_1>` <ARG_1_DESCRIPTION>
- `<ARG_2>` <ARG_2_DESCRIPTION>
## Outputs
Results are stored in the following folder of the [CAPS hierarchy](docs/CAPS): `subjects/sub-<participant_label>/ses-<session_label>/<some_folder>`.
The main output files are:
- `<source_file>_main_ouput_1`: description main output 1.
- `<source_file>_main_ouput_2`: description main output 2.
The full list of output files can be found in the [ClinicA Processed Structure (CAPS) Specification](https://docs.google.com/document/d/14mjXbqRceHK0fD0BIONniLK713zY7DbQHJEV7kxqsd8/edit#heading=h.f4ddnk971gkn).
## Visualization of the results
After the execution of the pipeline, you can check the outputs of a subject by running the command:
> **Notes:**
>
> _The visualization command is not available for the moment. Please come back later, this section will be updated ASAP._
## Describing this pipeline in your paper
> **Example of paragraph:**
>
>_These results have been obtained using the my-pipeline pipeline of Clinica. More precisely ..._
## Appendix
Further information can be found on [this supplementary page](docs/Pipelines/<My_Pipeline_Appendix>).
\ No newline at end of file
{
"id": "aramislab/t1-volume-parcellation",
"author": "John DOE",
"author": "Simona Bottani",
"version": "0.1.0",
"dependencies": [
{
......
......@@ -32,7 +32,7 @@ class T1VolumeParcellationCLI(ce.CmdParser):
self._args.add_argument("caps_directory",
help='Path to the CAPS directory.')
self._args.add_argument("group_id",
help = 'Current group name')
help='User-defined identifier for the provided group of subjects.')
self._args.add_argument("-tsv", "--subjects_sessions_tsv",
help='TSV file containing a list of subjects with their sessions.')
#self._args.add_argument("-im_type", "--image_type", type = str, default = 'T1',
......
# coding: utf8
"""spm_parcellation - Clinica Pipeline.
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.pipelines.engine as cpe
__author__ = "Simona Bottani"
......@@ -18,17 +12,8 @@ __email__ = "simona.bottani@icm-institute.org"
__status__ = "Development"
class T1VolumeParcellation(cpe.Pipeline):
"""spm_parcellation SHORT DESCRIPTION.
Warnings:
- A WARNING.
Todos:
- [x] A FILLED TODO ITEM.
- [ ] AN ON-GOING TODO ITEM.
"""T1 Volume parcellation
Args:
input_dir: A BIDS directory.
......@@ -84,14 +69,6 @@ class T1VolumeParcellation(cpe.Pipeline):
import nipype.pipeline.engine as npe
from clinica.lib.pycaps.caps_layout import CAPSLayout
# This node is supposedly used to load BIDS inputs when this pipeline is
# not already connected to the output of a previous Clinica pipeline.
# For the purpose of the example, we simply read input arguments given
# by the command line interface and transmitted here through the
# `self.parameters` dictionary and pass it to the `self.input_node` to
# further by used as input of the core nodes.
read_parameters_node = npe.Node(name="LoadingCLIArguments",
interface=nutil.IdentityInterface(
fields=self.get_input_fields(),
......
# coding: utf8
"""spm_parcellation - Clinica Utilities.
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"]
......@@ -19,7 +11,7 @@ __status__ = "Development"
def atlas_statistics(file_list, atlas_list):
"""
For each atlas name provided it ƒcalculates for the input image the mean for each region in the atlas and saves it to a tsv file.
For each atlas name provided it ƒcalculates for the input image the mean for each region in the atlas and saves it to a TSV file.
:param in_image: A Nifti image
:param in_atlas_list: List of names of atlas to be applied
:return: List of paths to tsv files
......
......@@ -26,6 +26,8 @@ class {{ pipeline.class_name }}CLI(ce.CmdParser):
# help='Path to the BIDS directory.')
# self._args.add_argument("caps_directory",
# help='Path to the CAPS directory.')
# self._args.add_argument("group_id",
# help='User-defined identifier for the provided group of subjects.')
# self._args.add_argument("-tsv", "--subjects_sessions_tsv",
# help='TSV file containing a list of subjects with their sessions.')
# Add your own pipeline command line arguments here to be used in the
......
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