Commit 31c05435 by simonabottani

Update T1 SPM Parcellation

parent a3a05dbf
Pipeline #938 passed with stages
in 33 seconds
......@@ -28,7 +28,7 @@
},
{
"name": "modulation",
"pattern":".*\/.*T1w_segm-graymatter_space-Ixi549Space_modulated-([a-z]+)_probability.nii.*"
"pattern":".*\/.*T1w_segm-graymatter_space-Ixi549Space_modulated-on_probability.nii.*"
}
]
......
......@@ -38,12 +38,6 @@ class T1VolumeParcellationCLI(ce.CmdParser):
#self._args.add_argument("-im_type", "--image_type", type = str, default = 'T1',
# choices =['T1', 'pet'],
# help = 'image type. Possible values are T1 and pet')
self._args.add_argument("-pet", "--pet_type", type = str, default = 'fdg',
choices = ['fdg', 'av45'],
help = 'PET image type. Possible values are fdg and av45.')
self._args.add_argument("-m", "--modulate", default='on',
choices=['on', 'off'],
help='A boolean. Modulate output images - no modulation preserves concentrations')
self._args.add_argument("-atlases", "--atlases", nargs='+', type=str,
default=['AAL2', 'LPBA40', 'Neuromorphometrics', 'AICHA', 'Hammers'],
choices=['AAL2', 'LPBA40', 'Neuromorphometrics', 'AICHA', 'Hammers'],
......@@ -72,8 +66,6 @@ class T1VolumeParcellationCLI(ce.CmdParser):
# pipeline. See the file `spm_parcellation_pipeline.py` to
# see an example of use.
'group_id': args.group_id,
'pet_type': args.pet_type,
'modulate': args.modulate,
'atlases': args.atlases,
'wd': self.absolute_path(args.working_directory),
'n_procs': args.n_procs
......
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