Commit 80edbd21 by simonabottani

Rename T1 Volume SPM pipeline

parent af8b0977
Pipeline #817 passed with stages
in 18 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_spm_segmentation.t1_spm_segmentation_cli import T1SPMSegmentationCLI # noqa
from clinica.pipelines.t1_volume_segmentation.t1_volume_segmentation_cli import T1VolumeSegmentationCLI # noqa
from clinica.pipelines.t1_spm_dartel.t1_spm_dartel_cli import T1SPMDartelCLI # noqa
from clinica.pipelines.t1_spm_dartel2mni.t1_spm_dartel2mni_cli import T1SPMDartel2MNICLI # noqa
from clinica.pipelines.t1_spm_full_prep.t1_spm_full_prep_cli import T1SPMFullPrepCLI # noqa
......@@ -136,7 +136,7 @@ def execute():
extra_dir="pipelines").load()
pipelines += [
T1FreeSurferCrossSectionalCLI(),
T1SPMSegmentationCLI(),
T1VolumeSegmentationCLI(),
T1SPMDartelCLI(),
T1SPMDartel2MNICLI(),
T1SPMFullPrepCLI(),
......
{
"id": "aramislab/t1-spm-segmentation",
"id": "aramislab/t1-volume-segmentation",
"author": "SAMPER-GONZALEZ Jorge",
"version": "0.1.0",
"dependencies": [
......
......@@ -18,7 +18,7 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1SPMSegmentationCLI(ce.CmdParser):
class T1VolumeSegmentationCLI(ce.CmdParser):
def define_name(self):
"""Define the sub-command name to run this pipelines.
......@@ -61,9 +61,9 @@ class T1SPMSegmentationCLI(ce.CmdParser):
def run_command(self, args):
"""
"""
from t1_spm_segmentation_pipeline import T1SPMSegmentation
from t1_volume_segmentation_pipeline import T1VolumeSegmentation
pipeline = T1SPMSegmentation(bids_directory=self.absolute_path(args.bids_directory),
pipeline = T1VolumeSegmentation(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 T1SPMSegmentation(cpe.Pipeline):
class T1VolumeSegmentation(cpe.Pipeline):
"""T1 SPM Segmentation SHORT DESCRIPTION.
Warnings:
......@@ -39,8 +39,8 @@ class T1SPMSegmentation(cpe.Pipeline):
Example:
>>> from t1_spm_segmentation import T1SPMSegmentation
>>> pipelines = T1SPMSegmentation('~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> from t1_volume_segmentation import T1VolumeSegmentation
>>> pipelines = T1VolumeSegmentation('~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> pipelines.parameters = {
>>> # ...
>>> }
......@@ -49,7 +49,7 @@ class T1SPMSegmentation(cpe.Pipeline):
"""
def __init__(self, bids_directory=None, caps_directory=None, tsv_file=None, name=None):
super(T1SPMSegmentation, self).__init__(bids_directory, caps_directory, tsv_file, name)
super(T1VolumeSegmentation, self).__init__(bids_directory, caps_directory, tsv_file, name)
# Default parameters
self._parameters = {'tissue_classes': [1, 2, 3],
'dartel_tissues': [1, 2, 3],
......@@ -102,7 +102,7 @@ class T1SPMSegmentation(cpe.Pipeline):
import nipype.pipeline.engine as npe
import nipype.interfaces.utility as nutil
import t1_spm_segmentation_utils as utils
import t1_volume_segmentation_utils as utils
# Reading BIDS
# ============
......@@ -120,7 +120,7 @@ class T1SPMSegmentation(cpe.Pipeline):
"""
import nipype.pipeline.engine as npe
import t1_spm_segmentation_utils as utils
import t1_volume_segmentation_utils as utils
import nipype.interfaces.io as nio
from clinica.utils.io import zip_nii
......@@ -193,7 +193,7 @@ class T1SPMSegmentation(cpe.Pipeline):
import nipype.interfaces.matlab as mlab
import nipype.pipeline.engine as npe
import nipype.interfaces.utility as nutil
import t1_spm_segmentation_utils as utils
import t1_volume_segmentation_utils as utils
from clinica.utils.io import unzip_nii
spm_home = os.getenv("SPM_HOME")
......
......@@ -147,7 +147,7 @@ class ApplySegmentationDeformation(SPMCommand):
Examples
--------
>>> import clinica.pipelines.t1_spm_segmentation.t1_spm_segmentation_utils as seg_utils
>>> import clinica.pipelines.t1_volume_segmentation.t1_volume_segmentation_utils as seg_utils
>>> inv = seg_utils.ApplySegmentationDeformation()
>>> inv.inputs.in_files = 'T1w.nii'
>>> inv.inputs.deformation = 'y_T1w.nii'
......
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