Merge remote-tracking branch 'origin/master'

clinica/pipelines/dwi_preprocessing_using_phasediff_fieldmap/dwi_preprocessing_using_phasediff_fieldmap_workflows.py

@@ -166,62 +166,62 @@ def susceptibility_distortion_correction_using_phasediff_fmap(
 
     wf = pe.Workflow(name=name)
     wf.connect([
-        (inputnode, fsl_dir, [('phase_encoding_direction', 'bids_dir')]),
-        (inputnode, pha2rads, [('in_fmap_phasediff', 'in_file')]),
-        (inputnode, get_b0,   [('in_dwi', 'in_file')]),
-        (inputnode, first_mag, [('in_fmap_magnitude', 'in_file')]),
-        (first_mag, n4, [('roi_file', 'input_image')]),
-        (n4, bet, [('output_image', 'in_file')]),
-        (bet, dilate, [('mask_file', 'in_file')]),
-        (pha2rads, prelude, [('out_file', 'phase_file')]),
-        (n4,       prelude, [('output_image', 'magnitude_file')]),
-        (dilate,   prelude, [('out_file', 'mask_file')]),
-        (prelude,   rad2rsec, [('unwrapped_phase_file', 'in_file')]),
-        (inputnode, rad2rsec, [('delta_echo_time', 'delta_te')]),
+        (inputnode, fsl_dir, [('phase_encoding_direction', 'bids_dir')]),  # noqa
+        (inputnode, pha2rads, [('in_fmap_phasediff', 'in_file')]),  # noqa
+        (inputnode, get_b0,   [('in_dwi', 'in_file')]),  # noqa
+        (inputnode, first_mag, [('in_fmap_magnitude', 'in_file')]),  # noqa
+        (first_mag, n4, [('roi_file', 'input_image')]),  # noqa
+        (n4, bet, [('output_image', 'in_file')]),  # noqa
+        (bet, dilate, [('mask_file', 'in_file')]),  # noqa
+        (pha2rads, prelude, [('out_file',     'phase_file')]),  # noqa
+        (n4,       prelude, [('output_image', 'magnitude_file')]),  # noqa
+        (dilate,   prelude, [('out_file',     'mask_file')]),  # noqa
+        (prelude,   rad2rsec, [('unwrapped_phase_file', 'in_file')]),  # noqa
+        (inputnode, rad2rsec, [('delta_echo_time',      'delta_te')]),  # noqa
     ])
     if register_fmap_on_b0:
         wf.connect([
-            (get_b0,    fmm2b0, [('roi_file', 'fixed_image')]),
-            (n4,        fmm2b0, [('output_image', 'moving_image')]),
-            (inputnode, fmm2b0, [('in_mask', 'fixed_image_mask')]),
-            (dilate,    fmm2b0, [('out_file', 'moving_image_mask')]),
-            (get_b0,   apply_xfm, [('roi_file', 'reference_image')]),
-            (rad2rsec, apply_xfm, [('out_file', 'input_image')]),
-            (fmm2b0,   apply_xfm, [('forward_transforms', 'transforms'),
-                                   ('forward_invert_flags', 'invert_transform_flags')]),
-            (apply_xfm, pre_fugue, [('output_image', 'fmap_in_file')]),
-            (inputnode, pre_fugue, [('in_mask', 'mask_file')]),
+            (get_b0,    fmm2b0, [('roi_file',     'fixed_image')]),  # noqa
+            (n4,        fmm2b0, [('output_image', 'moving_image')]),  # noqa
+            (inputnode, fmm2b0, [('in_mask',      'fixed_image_mask')]),  # noqa
+            (dilate,    fmm2b0, [('out_file',     'moving_image_mask')]),  # noqa
+            (get_b0,   apply_xfm, [('roi_file',            'reference_image')]),  # noqa
+            (rad2rsec, apply_xfm, [('out_file',            'input_image')]),  # noqa
+            (fmm2b0,   apply_xfm, [('forward_transforms',  'transforms'),  # noqa
+                                   ('forward_invert_flags', 'invert_transform_flags')]),  # noqa
+            (apply_xfm, pre_fugue, [('output_image', 'fmap_in_file')]),  # noqa
+            (inputnode, pre_fugue, [('in_mask', 'mask_file')]),  # noqa
 
             (apply_xfm, outputnode, [('output_image', 'out_prepared_fmap')])  # noqa
         ])
     else:
         wf.connect([
-            (get_b0,    res_fmap, [('roi_file', 'in_b0')]),
-            (rad2rsec,  res_fmap, [('out_file', 'in_fmap')]),
-            (res_fmap,  pre_fugue, [('out_resampled_fmap', 'fmap_in_file')]),
-            (inputnode, pre_fugue, [('in_mask', 'mask_file')]),
+            (get_b0,   res_fmap, [('roi_file', 'in_b0')]),  # noqa
+            (rad2rsec, res_fmap, [('out_file', 'in_fmap')]),  # noqa
+            (res_fmap,  pre_fugue, [('out_resampled_fmap', 'fmap_in_file')]),  # noqa
+            (inputnode, pre_fugue, [('in_mask',            'mask_file')]),  # noqa
 
             (res_fmap, outputnode, [('out_resampled_fmap', 'out_prepared_fmap')])  # noqa
         ])
     wf.connect([
-        (pre_fugue, demean, [('fmap_out_file', 'in_file')]),
-        (inputnode, demean, [('in_mask', 'in_mask')]),
-        (demean, cleanup, [('out_file', 'inputnode.in_file')]),
-        (inputnode, cleanup, [('in_mask', 'inputnode.in_mask')]),
-        (cleanup, add_vol, [('outputnode.out_file', 'in_file')]),
-        (inputnode, vsm, [('in_mask', 'mask_file')]),
-        (add_vol, vsm, [('out_file', 'fmap_in_file')]),
-        (inputnode, vsm, [('delta_echo_time', 'asym_se_time')]),
-        (inputnode, vsm, [('effective_echo_spacing', 'dwell_time')]),
-        (inputnode, split, [('in_dwi', 'in_file')]),
-        (split, unwarp, [('out_files', 'in_file')]),
-        (vsm, unwarp, [('shift_out_file', 'shift_in_file')]),
-        (fsl_dir, unwarp, [('fsl_dir', 'unwarp_direction')]),
-        (unwarp, thres, [('unwarped_file', 'in_file')]),
-        (thres, merge, [('out_file', 'in_files')]),
-        (merge, vsm2dfm, [('merged_file', 'inputnode.in_ref')]),
-        (vsm, vsm2dfm, [('shift_out_file', 'inputnode.in_vsm')]),
-        (fsl_dir, vsm2dfm, [('fsl_dir', 'inputnode.enc_dir')]),
+        (pre_fugue, demean, [('fmap_out_file', 'in_file')]),  # noqa
+        (inputnode, demean, [('in_mask', 'in_mask')]),  # noqa
+        (demean,    cleanup, [('out_file', 'inputnode.in_file')]),  # noqa
+        (inputnode, cleanup, [('in_mask',  'inputnode.in_mask')]),  # noqa
+        (cleanup, add_vol, [('outputnode.out_file', 'in_file')]),  # noqa
+        (inputnode, vsm, [('in_mask',                'mask_file')]),  # noqa
+        (add_vol,   vsm, [('out_file',               'fmap_in_file')]),  # noqa
+        (inputnode, vsm, [('delta_echo_time',        'asym_se_time')]),  # noqa
+        (inputnode, vsm, [('effective_echo_spacing', 'dwell_time')]),  # noqa
+        (inputnode, split, [('in_dwi', 'in_file')]),  # noqa
+        (split,   unwarp, [('out_files',      'in_file')]),  # noqa
+        (vsm,     unwarp, [('shift_out_file', 'shift_in_file')]),  # noqa
+        (fsl_dir, unwarp, [('fsl_dir',        'unwarp_direction')]),  # noqa
+        (unwarp, thres, [('unwarped_file', 'in_file')]),  # noqa
+        (thres, merge, [('out_file', 'in_files')]),  # noqa
+        (merge,   vsm2dfm, [('merged_file',    'inputnode.in_ref')]),  # noqa
+        (vsm,     vsm2dfm, [('shift_out_file', 'inputnode.in_vsm')]),  # noqa
+        (fsl_dir, vsm2dfm, [('fsl_dir',        'inputnode.enc_dir')]),  # noqa
         (rad2rsec, outputnode, [('out_file',            'out_native_fmap')]),  # noqa
         (merge,    outputnode, [('merged_file',         'out_file')]),  # noqa
         (vsm,      outputnode, [('shift_out_file',      'out_vsm')]),  # noqa

clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_pipeline.py

 # coding: utf8
 
-
 import clinica.pipelines.engine as cpe
 
 __author__ = ["Thomas Jacquemont", "Alexandre Routier"]
@@ -31,14 +30,13 @@ class DWIPreprocessingUsingT1(cpe.Pipeline):
 
 
     Example:
-        >>> from dwi_preprocessing_using_t1 import DWIPreprocessingUsingT1
-        >>> pipelines = DWIPreprocessingUsingT1('~/MYDATASET_BIDS',
+        >>> pipeline = DWIPreprocessingUsingT1('~/MYDATASET_BIDS',
         >>>                                    '~/MYDATASET_CAPS')
-        >>> pipelines.parameters = {
+        >>> pipeline.parameters = {
         >>>     'low_bval': 10
         >>> }
-        >>> pipelines.base_dir = '/tmp/'
-        >>> pipelines.run()
+        >>> pipeline.base_dir = '/tmp/'
+        >>> pipeline.run()
     """
     def __init__(self, bids_directory=None, caps_directory=None, tsv_file=None,
                  name=None, low_bval=5):
@@ -347,36 +345,36 @@ class DWIPreprocessingUsingT1(cpe.Pipeline):
 
         self.connect([
             # Preliminary step (possible computation of a mean b0):
-            (self.input_node, prepare_b0, [('dwi', 'in_dwi'),
-                                           ('bval', 'in_bval'),
-                                           ('bvec', 'in_bvec')]),
+            (self.input_node, prepare_b0, [('dwi',  'in_dwi'),  # noqa
+                                           ('bval', 'in_bval'),  # noqa
+                                           ('bvec', 'in_bvec')]),  # noqa
             # Mask b0 before corrections
-            (prepare_b0, mask_b0_pre, [('out_reference_b0', 'in_file')]),
+            (prepare_b0, mask_b0_pre, [('out_reference_b0', 'in_file')]),  # noqa
             # Head-motion correction
-            (prepare_b0, hmc, [('out_b0_dwi_merge', 'inputnode.in_file'),
-                               ('out_updated_bval', 'inputnode.in_bval'),
-                               ('out_updated_bvec', 'inputnode.in_bvec')]),
-            (mask_b0_pre, hmc, [('mask_file', 'inputnode.in_mask')]),
+            (prepare_b0,  hmc, [('out_b0_dwi_merge', 'inputnode.in_file'),  # noqa
+                               ('out_updated_bval',  'inputnode.in_bval'),  # noqa
+                               ('out_updated_bvec',  'inputnode.in_bvec')]),  # noqa
+            (mask_b0_pre, hmc, [('mask_file',        'inputnode.in_mask')]),  # noqa
 
             # Eddy-current correction
-            (hmc, ecc, [('outputnode.out_xfms', 'inputnode.in_xfms')]),
-            (prepare_b0, ecc, [('out_b0_dwi_merge', 'inputnode.in_file')]),
-            (prepare_b0, ecc, [('out_updated_bval', 'inputnode.in_bval')]),
-            (mask_b0_pre, ecc, [('mask_file', 'inputnode.in_mask')]),
+            (hmc,         ecc, [('outputnode.out_xfms', 'inputnode.in_xfms')]),  # noqa
+            (prepare_b0,  ecc, [('out_b0_dwi_merge',    'inputnode.in_file')]),  # noqa
+            (prepare_b0,  ecc, [('out_updated_bval',    'inputnode.in_bval')]),  # noqa
+            (mask_b0_pre, ecc, [('mask_file',           'inputnode.in_mask')]),  # noqa
             # Magnetic susceptibility correction
-            (ecc, sdc, [('outputnode.out_file', 'inputnode.in_dwi')]),
-            (self.input_node, sdc, [('T1w', 'inputnode.in_t1')]),
+            (ecc,             sdc, [('outputnode.out_file', 'inputnode.in_dwi')]),  # noqa
+            (self.input_node, sdc, [('T1w',                 'inputnode.in_t1')]),  # noqa
             # Apply all corrections
-            (prepare_b0, aac, [('out_b0_dwi_merge', 'inputnode.in_dwi')]),
-            (hmc, aac, [('outputnode.out_xfms', 'inputnode.in_hmc')]),
-            (ecc, aac, [('outputnode.out_xfms', 'inputnode.in_ecc')]),
-            (sdc, aac, [('outputnode.out_warp', 'inputnode.in_sdc_syb')]),
-            (self.input_node, aac, [('T1w', 'inputnode.in_t1')]),
+            (prepare_b0,      aac, [('out_b0_dwi_merge',    'inputnode.in_dwi')]),  # noqa
+            (hmc,             aac, [('outputnode.out_xfms', 'inputnode.in_hmc')]),  # noqa
+            (ecc,             aac, [('outputnode.out_xfms', 'inputnode.in_ecc')]),  # noqa
+            (sdc,             aac, [('outputnode.out_warp', 'inputnode.in_sdc_syb')]),  # noqa
+            (self.input_node, aac, [('T1w',                 'inputnode.in_t1')]),  # noqa
             # Bias correction
             (aac, bias, [('outputnode.out_file', 'inputnode.in_file')]),
             # Outputnode:
-            (bias,       self.output_node, [('outputnode.out_file',  'preproc_dwi')]),  # noqa
+            (bias,       self.output_node, [('outputnode.out_file', 'preproc_dwi')]),  # noqa
             (hmc,        self.output_node, [('outputnode.out_bvec', 'preproc_bvec')]),  # noqa
             (prepare_b0, self.output_node, [('out_updated_bval',    'preproc_bval')]),  # noqa
-            (bias,       self.output_node, [('outputnode.b0_mask',       'b0_mask')])   # noqa
+            (bias,       self.output_node, [('outputnode.b0_mask',  'b0_mask')])   # noqa
         ])

clinica/pipelines/dwi_processing_dti/dwi_processing_dti_cli.py

@@ -11,7 +11,14 @@ class DWIProcessingDTICLI(ce.CmdParser):
     def define_name(self):
         """Define the sub-command name to run this pipeline.
         """
+        from colorama import Fore, init
+        init()
+
         self._name = 'dwi-processing-dti'
+        self._args.epilog = 'Example: clinica run dwi-processing-dti BIDS CAPS'
+        self._args.description = "%sDTI-based pipeline: http:://clinica.run/doc/DWIProcessing%s" % (Fore.GREEN, Fore.RESET)
+        self._args._positionals.title = '%sCompulsory arguments:%s' % (Fore.BLUE, Fore.RESET)
+        self._args._optionals.title = '%sOptional arguments:%s' % (Fore.BLUE, Fore.RESET)
 
     def define_options(self):
         """Define the sub-command arguments