Skip to content

Commit 89d3059

Browse files
mfmachadomfmachado
committed
Added more variable descriptions.
1 parent ea72f5e commit 89d3059

File tree

1 file changed

+37
-27
lines changed

1 file changed

+37
-27
lines changed

‎nipype/interfaces/cat12/preprocess.py

Lines changed: 37 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,6 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
1818
copyfile=False)
1919

2020
n_jobs = traits.Int(1, usedefault=True, mandatory=True, field="nproc", desc="Number of threads")
21-
use_prior = Str(field="useprior", usedefault=True)
2221

2322
_help_affine_reg = 'Affine Regularization. The procedure is a local optimisation, so it needs reasonable initial ' \
2423
'starting estimates. Images should be placed in approximate alignment using the Display ' \
@@ -129,64 +128,75 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
129128
'further analysis! For distinction, these files contain "preview" in their filename and they' \
130129
' are not available as batch dependencies objects. '
131130
surface_and_thickness_estimation = traits.Int(1, field="surface", desc=_help_surf, usedefault=True)
132-
surface_measures = traits.Int(1, field="output.surf_measures", usedefault=True)
131+
surface_measures = traits.Int(1, field="output.surf_measures", usedefault=True, desc="Extract surface measures")
133132

134133
# Templates
135134
neuromorphometrics = traits.Bool(True, field="output.ROImenu.atlases.neuromorphometrics",
136-
usedefault=True)
137-
lpba40 = traits.Bool(True, field="output.ROImenu.atlases.lpba40", usedefault=True)
138-
cobra = traits.Bool(True, field="output.ROImenu.atlases.hammers", usedefault=True)
139-
hammers = traits.Bool(True, field="output.ROImenu.atlases.cobra", usedefault=True)
135+
usedefault=True, desc="Extract brain measures for Neuromorphometrics template")
136+
lpba40 = traits.Bool(True, field="output.ROImenu.atlases.lpba40", usedefault=True,
137+
desc="Extract brain measures for LPBA40 template")
138+
cobra = traits.Bool(True, field="output.ROImenu.atlases.hammers", usedefault=True,
139+
desc="Extract brain measures for COBRA template")
140+
hammers = traits.Bool(True, field="output.ROImenu.atlases.cobra", usedefault=True,
141+
desc="Extract brain measures for Hammers template")
140142
own_atlas = InputMultiPath(ImageFileSPM(exists=True), field="output.ROImenu.atlases.ownatlas",
141-
desc="Own Atlas", mandatory=False, copyfile=False)
143+
desc="Extract brain measures for a given template", mandatory=False, copyfile=False)
142144

143145
_dartel_help = 'This option is to export data into a form that can be used with DARTEL. The SPM default is to ' \
144146
'only apply rigid body transformation. However, a more appropriate option is to apply affine ' \
145147
'transformation, because the additional scaling of the images requires less deformations to ' \
146148
'non-linearly register brains to the template.'
147149

148150
# Grey matter
149-
_gm_desc = 'Options to save grey matter images.'
150-
gm_output_native = traits.Bool(False, field="output.GM.native", usedefault=True, desc=_gm_desc)
151-
gm_output_modulated = traits.Bool(True, field="output.GM.mod", usedefault=True, desc=_gm_desc)
152-
gm_output_dartel = traits.Bool(False, field="output.GM.dartel", usedefault=True, desc=_gm_desc)
151+
gm_output_native = traits.Bool(False, field="output.GM.native", usedefault=True,
152+
desc='Save modulated grey matter images.')
153+
gm_output_modulated = traits.Bool(True, field="output.GM.mod", usedefault=True,
154+
desc='Save native grey matter images.')
155+
gm_output_dartel = traits.Bool(False, field="output.GM.dartel", usedefault=True,
156+
desc='Save dartel grey matter images.')
153157

154158
# White matter
155159
_wm_desc = 'Options to save white matter images.'
156-
wm_output_native = traits.Bool(False, field="output.WM.native", usedefault=True, desc=_wm_desc)
157-
wm_output_modulated = traits.Bool(True, field="output.WM.mod", usedefault=True, desc=_wm_desc)
158-
wm_output_dartel = traits.Bool(False, field="output.WM.dartel", usedefault=True, desc=_wm_desc)
160+
wm_output_native = traits.Bool(False, field="output.WM.native", usedefault=True,
161+
desc='Save dartel white matter images.')
162+
wm_output_modulated = traits.Bool(True, field="output.WM.mod", usedefault=True,
163+
desc='Save dartel white matter images.')
164+
wm_output_dartel = traits.Bool(False, field="output.WM.dartel", usedefault=True,
165+
desc='Save dartel white matter images.')
159166

160167
# CSF matter
161168
_csf_desc = 'Options to save CSF images.'
162-
csf_output_native = traits.Bool(False, field="output.CSF.native", usedefault=True, desc=_csf_desc)
163-
csf_output_modulated = traits.Bool(True, field="output.CSF.mod", usedefault=True, desc=_csf_desc)
164-
csf_output_dartel = traits.Bool(False, field="output.CSF.dartel", usedefault=True, desc=_csf_desc)
169+
csf_output_native = traits.Bool(False, field="output.CSF.native", usedefault=True,
170+
desc='Save dartel CSF images.')
171+
csf_output_modulated = traits.Bool(True, field="output.CSF.mod", usedefault=True,
172+
desc='Save dartel CSF images.')
173+
csf_output_dartel = traits.Bool(False, field="output.CSF.dartel", usedefault=True,
174+
desc='Save dartel CSF images.')
165175

166176
# Labels
167-
_help_label_desc = 'This is the option to save a labeled version of your segmentations for fast visual ' \
177+
_help_label_desc = 'This is the option to save a labeled version of your segmentations in the %s space for fast visual ' \
168178
'comparision. Labels are saved as Partial Volume Estimation (PVE) values with different mix ' \
169179
'classes for GM-WM (2.5) and GM-CSF (1.5). BG=0, CSF=1, GM=2, WM=3, WMH=4 (if WMHC=3), ' \
170180
'SL=1.5 (if SLC)'
171-
label_native = traits.Bool(False, field="output.label.native", usedefault=True, desc=_help_label_desc)
172-
label_warped = traits.Bool(True, field="output.label.warped", usedefault=True, desc=_help_label_desc)
173-
label_dartel = traits.Bool(False, field="output.label.dartel", usedefault=True, desc=_help_label_desc)
174-
output_labelnative = traits.Bool(False, field="output.labelnative", usedefault=True, desc=_help_label_desc)
181+
label_native = traits.Bool(False, field="output.label.native", usedefault=True, desc=_help_label_desc % "native")
182+
label_warped = traits.Bool(True, field="output.label.warped", usedefault=True, desc=_help_label_desc % "warped")
183+
label_dartel = traits.Bool(False, field="output.label.dartel", usedefault=True, desc=_help_label_desc % "dartel")
184+
output_labelnative = traits.Bool(False, field="output.labelnative", usedefault=True, desc=_help_label_desc % "native")
175185

176186
# Bias
177-
save_bias_corrected = traits.Bool(True, field="output.bias.warped", usedefault=True)
187+
save_bias_corrected = traits.Bool(True, field="output.bias.warped", usedefault=True, desc="Save bias corrected image")
178188

179189
# las
180190
_las_desc = 'This is the option to save a bias, noise, and local intensity corrected version of the original T1' \
181-
' image. MR images are usually corrupted by a smooth, spatially varying artifact that modulates the' \
191+
' image in the %s space. MR images are usually corrupted by a smooth, spatially varying artifact that modulates the' \
182192
' intensity of the image (bias). These artifacts, although not usually a problem for visual ' \
183193
'inspection, can impede automated processing of the images. The bias corrected version should have ' \
184194
'more uniform intensities within the different types of tissues and can be saved in native space ' \
185195
'and/or normalised. Noise is corrected by an adaptive non-local mean (NLM) filter (Manjon 2008, ' \
186196
'Medical Image Analysis 12).'
187-
las_native = traits.Bool(False, field="output.las.native", usedefault=True, desc=_las_desc)
188-
las_warped = traits.Bool(True, field="output.las.warped", usedefault=True, desc=_las_desc)
189-
las_dartel = traits.Bool(False, field="output.las.dartel", usedefault=True, desc=_las_desc)
197+
las_native = traits.Bool(False, field="output.las.native", usedefault=True, desc=_las_desc % "native")
198+
las_warped = traits.Bool(True, field="output.las.warped", usedefault=True, desc=_las_desc % "warped")
199+
las_dartel = traits.Bool(False, field="output.las.dartel", usedefault=True, desc=_las_desc % "dartel")
190200

191201
# Jacobian Warped
192202
_help_jacobian = 'This is the option to save the Jacobian determinant, which expresses local volume changes. This' \

0 commit comments

Comments
 (0)