Commit 9d9dc596 by simonabottani

Rename T1 Volume Pipelines

parent 7c5fd3e5
Pipeline #820 failed with stages
in 15 seconds
......@@ -119,7 +119,7 @@ def execute():
from clinica.engine import CmdParser
from clinica.pipelines.t1_freesurfer_cross_sectional.t1_freesurfer_cross_sectional_cli import T1FreeSurferCrossSectionalCLI # noqa
from clinica.pipelines.t1_volume_segmentation.t1_volume_segmentation_cli import T1VolumeSegmentationCLI # noqa
from clinica.pipelines.t1_volume_tissue_segmentation.t1_volume_tissue_segmentation_cli import T1VolumeTissueSegmentationCLI # noqa
from clinica.pipelines.t1_volume_create_dartel.t1_volume_create_dartel_cli import T1VolumeCreateDartelCLI # noqa
from clinica.pipelines.t1_volume_dartel2mni.t1_volume_dartel2mni_cli import T1VolumeDartel2MNICLI # noqa
from clinica.pipelines.t1_volume_new_template.t1_volume_new_template_cli import T1VolumeNewTemplateCLI # noqa
......
{
"id": "aramislab/t1-volume-segmentation",
"id": "aramislab/t1-volume-tissue-segmentation",
"author": "SAMPER-GONZALEZ Jorge",
"version": "0.1.0",
"dependencies": [
......
......@@ -18,12 +18,12 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1VolumeSegmentationCLI(ce.CmdParser):
class T1VolumeTissueSegmentationCLI(ce.CmdParser):
def define_name(self):
"""Define the sub-command name to run this pipelines.
"""
self._name = 't1-volume-segmentation'
self._name = 't1-volume-tissue-segmentation'
def define_description(self):
"""Define a description of this pipeline.
......@@ -61,9 +61,9 @@ class T1VolumeSegmentationCLI(ce.CmdParser):
def run_command(self, args):
"""
"""
from t1_volume_segmentation_pipeline import T1VolumeSegmentation
from t1_volume_tissue_segmentation_pipeline import T1VolumeTissueSegmentation
pipeline = T1VolumeSegmentation(bids_directory=self.absolute_path(args.bids_directory),
pipeline = T1VolumeTissueSegmentation(bids_directory=self.absolute_path(args.bids_directory),
caps_directory=self.absolute_path(args.caps_directory),
tsv_file=self.absolute_path(args.subjects_sessions_tsv))
......
......@@ -17,7 +17,7 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1VolumeSegmentation(cpe.Pipeline):
class T1VolumeTissueSegmentation(cpe.Pipeline):
"""T1 SPM Segmentation SHORT DESCRIPTION.
Warnings:
......@@ -39,7 +39,7 @@ class T1VolumeSegmentation(cpe.Pipeline):
Example:
>>> from t1_volume_segmentation import T1VolumeSegmentation
>>> from t1_volume_tissue_segmentation import T1VolumeTissueSegmentation
>>> pipelines = T1VolumeSegmentation('~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> pipelines.parameters = {
>>> # ...
......@@ -49,7 +49,7 @@ class T1VolumeSegmentation(cpe.Pipeline):
"""
def __init__(self, bids_directory=None, caps_directory=None, tsv_file=None, name=None):
super(T1VolumeSegmentation, self).__init__(bids_directory, caps_directory, tsv_file, name)
super(T1VolumeTissueSegmentation, self).__init__(bids_directory, caps_directory, tsv_file, name)
# Default parameters
self._parameters = {'tissue_classes': [1, 2, 3],
'dartel_tissues': [1, 2, 3],
......@@ -193,7 +193,7 @@ class T1VolumeSegmentation(cpe.Pipeline):
import nipype.interfaces.matlab as mlab
import nipype.pipeline.engine as npe
import nipype.interfaces.utility as nutil
import t1_volume_segmentation_utils as utils
import t1_volume_tissue_segmentation_utils as utils
from clinica.utils.io import unzip_nii
spm_home = os.getenv("SPM_HOME")
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment