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David Ellis
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FIX: Changes the setting of the workflow configurations to run time.
1 parent 4538eb5 commit 87c9ed3

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3 files changed

+158
-52
lines changed

3 files changed

+158
-52
lines changed

‎nipype/workflows/smri/freesurfer/autorecon1.py‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -54,7 +54,7 @@ def checkT1s(T1_files, cw256=False):
5454
return T1_files, cw256, resample_type, origvol_names
5555

5656
def create_AutoRecon1(name="AutoRecon1", longitudinal=False, field_strength='1.5T',
57-
custom_atlas=None, awk_file=None, plugin_args=None):
57+
custom_atlas=None, plugin_args=None):
5858
"""Creates the AutoRecon1 workflow in nipype.
5959
6060
Inputs::
@@ -72,7 +72,8 @@ def create_AutoRecon1(name="AutoRecon1", longitudinal=False, field_strength='1.5
7272
'FLAIR_file',
7373
'cw256',
7474
'num_threads',
75-
'reg_template_withskull']),
75+
'reg_template_withskull',
76+
'awk_file']),
7677
run_without_submitting=True,
7778
name='inputspec')
7879

@@ -337,7 +338,7 @@ def createTemplate(in_files, out_file):
337338
ar1_wf.connect([(copy_transform, check_alignment, [('out_file', 'in_file')]),
338339
])
339340

340-
if not longitudinal and awk_file:
341+
if not longitudinal:
341342
def awkfile(in_file, log_file):
342343
"""
343344
This method uses 'awk' which must be installed prior to running the workflow and is not a
@@ -355,9 +356,9 @@ def awkfile(in_file, log_file):
355356
['log_file'],
356357
awkfile),
357358
name='Awk')
358-
awk_logfile.inputs.in_file = awk_file
359359

360-
ar1_wf.connect([(talairach_avi, awk_logfile, [('out_log', 'log_file')])])
360+
ar1_wf.connect([(talairach_avi, awk_logfile, [('out_log', 'log_file')]),
361+
(inputspec, awk_logfile, [('awk_file', 'in_file')])])
361362

362363
# TODO datasink the output from TalirachQC...not sure how to do this
363364
tal_qc = pe.Node(TalairachQC(), name="Detect_Aligment_Failures")

‎nipype/workflows/smri/freesurfer/autorecon2.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -697,7 +697,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
697697
(edit_wm, outputspec, [('out_file', 'wm_aseg')]),
698698
(pretess, outputspec, [('out_file', 'wm')]),
699699
(fill, outputspec, [('out_file', 'filled'),
700-
('log_file', 'ponscc.cut.log')]),
700+
('log_file', 'ponscc_log')]),
701701
])
702702

703703
for hemi, hemi_wf in [('lh', ar2_lh), ('rh', ar2_rh)]:

‎nipype/workflows/smri/freesurfer/recon.py‎

Lines changed: 151 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -79,17 +79,32 @@ def link_masks(subjects_dir, subject_id):
7979
wf.connect(autorecon_resume, "subject_id", outputnode, "subject_id")
8080
return wf
8181

82-
def create_reconall_workflow(name="ReconAll", plugin_args=None):
82+
def create_reconall_workflow(name="ReconAll", plugin_args=None,
83+
recoding_file=None):
8384
"""Creates the ReconAll workflow in nipype.
85+
86+
Example
87+
-------
88+
>>> from nipype.workflows.smri.freesurfer import create_skullstripped_recon_flow
89+
>>> import nipype.interfaces.freesurfer as fs
90+
>>> recon_all = create_skullstripped_recon_flow()
91+
>>> recon_all.inputs.inputspec.subject_id = 'subj1'
92+
>>> recon_all.inputs.inputspec.subjects_dir = '.'
93+
>>> recon_all.inputs.inputspec.T1_files = 'T1.nii.gz'
94+
>>> recon_flow.run() # doctest: +SKIP
95+
8496
8597
Inputs::
98+
inputspec.subjects_dir : subjects directory (mandatory)
99+
inputspec.subject_id : name of subject (mandatory)
86100
inputspec.T1_files : T1 files (mandatory)
87101
inputspec.T2_file : T2 file (optional)
88102
inputspec.FLAIR_file : FLAIR file (optional)
89103
inputspec.cw256 : Conform inputs to 256 FOV (optional)
90104
inputspec.num_threads: Number of threads on nodes that utilize OpenMP (default=1)
91105
plugin_args : Dictionary of plugin args to set to nodes that utilize OpenMP (optional)
92106
Outpus::
107+
postdatasink_outputspec.subject_id : name of the datasinked output folder in the subjects directory
93108
94109
"""
95110
reconall = pe.Workflow(name=name)
@@ -115,66 +130,122 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None):
115130
'wm_lookup_table',
116131
'src_subject_id',
117132
'src_subject_dir',
118-
'color_table']),
133+
'color_table',
134+
'awk_file']),
119135
run_without_submitting=True,
120136
name='inputspec')
121137

122-
# get the default configurations
123-
defaultconfig = getdefaultconfig()
124-
125-
# set the default template and classifier files
126-
inputspec.inputs.reg_template = defaultconfig['registration_template']
127-
inputspec.inputs.reg_template_withskull = defaultconfig['registration_template_withskull']
128-
inputspec.inputs.lh_atlas = defaultconfig['lh_atlas']
129-
inputspec.inputs.rh_atlas = defaultconfig['rh_atlas']
130-
inputspec.inputs.lh_classifier1 = defaultconfig['lh_classifier']
131-
inputspec.inputs.rh_classifier1 = defaultconfig['rh_classifier']
132-
inputspec.inputs.lh_classifier2 = defaultconfig['lh_classifier2']
133-
inputspec.inputs.rh_classifier2 = defaultconfig['rh_classifier2']
134-
inputspec.inputs.lh_classifier3 = defaultconfig['lh_classifier3']
135-
inputspec.inputs.rh_classifier3 = defaultconfig['rh_classifier3']
136-
inputspec.inputs.src_subject_id = defaultconfig['src_subject_id']
137-
inputspec.inputs.src_subject_dir = defaultconfig['src_subject_dir']
138-
inputspec.inputs.color_table = defaultconfig['AvgColorTable']
139-
inputspec.inputs.lookup_table = defaultconfig['LookUpTable']
140-
inputspec.inputs.wm_lookup_table = defaultconfig['WMLookUpTable']
138+
def setconfig(reg_template=None,
139+
reg_template_withskull=None,
140+
lh_atlas=None,
141+
rh_atlas=None,
142+
lh_classifier1=None,
143+
rh_classifier1=None,
144+
lh_classifier2=None,
145+
rh_classifier2=None,
146+
lh_classifier3=None,
147+
rh_classifier3=None,
148+
src_subject_id=None,
149+
src_subject_dir=None,
150+
color_table=None,
151+
lookup_table=None,
152+
wm_lookup_table=None,
153+
awk_file=None):
154+
"""Set optional configurations to the default"""
155+
from nipype.workflows.smri.freesurfer.utils import getdefaultconfig
156+
def checkarg(arg, default):
157+
"""Returns the value if defined; otherwise default"""
158+
if arg:
159+
return arg
160+
else:
161+
return default
162+
# set the default template and classifier files
163+
reg_template = checkarg(reg_template, defaultconfig['registration_template'])
164+
reg_template_withskull = checkarg(reg_template_withskull,
165+
defaultconfig['registration_template_withskull'])
166+
lh_atlas = checkarg(lh_atlas, defaultconfig['lh_atlas'])
167+
rh_atlas = checkarg(rh_atlas, defaultconfig['rh_atlas'])
168+
lh_classifier1 = checkarg(lh_classifier1, defaultconfig['lh_classifier'])
169+
rh_classifier1 = checkarg(rh_classifier1, defaultconfig['rh_classifier'])
170+
lh_classifier2 = checkarg(lh_classifier2, defaultconfig['lh_classifier2'])
171+
rh_classifier2 = checkarg(rh_classifier2, defaultconfig['rh_classifier2'])
172+
lh_classifier3 = checkarg(lh_classifier3, defaultconfig['lh_classifier3'])
173+
rh_classifier3 = checkarg(rh_classifier3, defaultconfig['rh_classifier3'])
174+
src_subject_id = checkarg(src_subject_id, defaultconfig['src_subject_id'])
175+
src_subject_dir = checkarg(src_subject_dir, defaultconfig['src_subject_dir'])
176+
color_table = checkarg(color_table, defaultconfig['AvgColorTable'])
177+
lookup_table = checkarg(lookup_table, defaultconfig['LookUpTable'])
178+
wm_lookup_table = checkarg(wm_lookup_table, defaultconfig['WMLookUpTable'])
179+
awk_file = checkarg(awk_file, defaultconfig['awk_file'])
180+
return reg_template, reg_template_withskull, lh_atlas, rh_atlas, \
181+
lh_classifier1, rh_classifier1, lh_classifier2, rh_classifier2, \
182+
lh_classifier3, rh_classifier3, src_subject_id, src_subject_dir, \
183+
color_table, lookup_table, wm_lookup_table, awk_file
184+
185+
# list of params to check
186+
params = ['reg_template',
187+
'reg_template_withskull',
188+
'lh_atlas',
189+
'rh_atlas',
190+
'lh_classifier1',
191+
'rh_classifier1',
192+
'lh_classifier2',
193+
'rh_classifier2',
194+
'lh_classifier3',
195+
'rh_classifier3',
196+
'lookup_table',
197+
'wm_lookup_table',
198+
'src_subject_id',
199+
'src_subject_dir',
200+
'color_table',
201+
'awk_file']
202+
203+
config_node = pe.Node(niu.Function(params,
204+
params,
205+
setconfig),
206+
name="config")
207+
208+
for param in params:
209+
reconall.connect(inputspec, param, config_node, param)
141210

142211
# create AutoRecon1
143-
ar1_wf, ar1_outputs = create_AutoRecon1(plugin_args=plugin_args,
144-
awk_file=defaultconfig['awk_file'])
212+
ar1_wf, ar1_outputs = create_AutoRecon1(plugin_args=plugin_args)
145213
# connect inputs for AutoRecon1
146214
reconall.connect([(inputspec, ar1_wf, [('T1_files', 'inputspec.T1_files'),
147215
('T2_file', 'inputspec.T2_file'),
148216
('FLAIR_file', 'inputspec.FLAIR_file'),
149217
('num_threads', 'inputspec.num_threads'),
150-
('cw256', 'inputspec.cw256'),
151-
('reg_template_withskull', 'inputspec.reg_template_withskull')])])
218+
('cw256', 'inputspec.cw256')]),
219+
(config_node, ar1_wf, [('reg_template_withskull',
220+
'inputspec.reg_template_withskull'),
221+
('awk_file', 'inputspec.awk_file')])])
152222

153223
# create AutoRecon2
154224
ar2_wf, ar2_outputs = create_AutoRecon2(plugin_args=plugin_args)
155225
# connect inputs for AutoRecon2
156-
reconall.connect([(inputspec, ar2_wf, [('num_threads', 'inputspec.num_threads'),
157-
('reg_template', 'inputspec.reg_template'),
158-
('reg_template_withskull', 'inputspec.reg_template_withskull')]),
226+
reconall.connect([(inputspec, ar2_wf, [('num_threads', 'inputspec.num_threads')]),
227+
(config_node, ar2_wf, [('reg_template_withskull',
228+
'inputspec.reg_template_withskull'),
229+
('reg_template', 'inputspec.reg_template')]),
159230
(ar1_wf, ar2_wf, [('outputspec.brainmask', 'inputspec.brainmask'),
160231
('outputspec.talairach', 'inputspec.transform'),
161232
('outputspec.orig', 'inputspec.orig')])])
162233
# create AutoRecon3
163-
ar3_wf, ar3_outputs = create_AutoRecon3(plugin_args=plugin_args, th3=defaultconfig['th3'])
234+
ar3_wf, ar3_outputs = create_AutoRecon3(plugin_args=plugin_args, th3=True)
164235
# connect inputs for AutoRecon3
165-
reconall.connect([(inputspec, ar3_wf, [('lh_atlas', 'inputspec.lh_atlas'),
166-
('rh_atlas', 'inputspec.rh_atlas'),
167-
('lh_classifier1', 'inputspec.lh_classifier1'),
168-
('rh_classifier1', 'inputspec.rh_classifier1'),
169-
('lh_classifier2', 'inputspec.lh_classifier2'),
170-
('rh_classifier2', 'inputspec.rh_classifier2'),
171-
('lh_classifier3', 'inputspec.lh_classifier3'),
172-
('rh_classifier3', 'inputspec.rh_classifier3'),
173-
('lookup_table', 'inputspec.lookup_table'),
174-
('wm_lookup_table', 'inputspec.wm_lookup_table'),
175-
('src_subject_dir', 'inputspec.src_subject_dir'),
176-
('src_subject_id', 'inputspec.src_subject_id'),
177-
('color_table', 'inputspec.color_table')]),
236+
reconall.connect([(config_node, ar3_wf, [('lh_atlas', 'inputspec.lh_atlas'),
237+
('rh_atlas', 'inputspec.rh_atlas'),
238+
('lh_classifier1', 'inputspec.lh_classifier1'),
239+
('rh_classifier1', 'inputspec.rh_classifier1'),
240+
('lh_classifier2', 'inputspec.lh_classifier2'),
241+
('rh_classifier2', 'inputspec.rh_classifier2'),
242+
('lh_classifier3', 'inputspec.lh_classifier3'),
243+
('rh_classifier3', 'inputspec.rh_classifier3'),
244+
('lookup_table', 'inputspec.lookup_table'),
245+
('wm_lookup_table', 'inputspec.wm_lookup_table'),
246+
('src_subject_dir', 'inputspec.src_subject_dir'),
247+
('src_subject_id', 'inputspec.src_subject_id'),
248+
('color_table', 'inputspec.color_table')]),
178249
(ar1_wf, ar3_wf, [('outputspec.brainmask', 'inputspec.brainmask'),
179250
('outputspec.talairach', 'inputspec.transform'),
180251
('outputspec.orig', 'inputspec.orig_mgz'),
@@ -209,7 +280,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None):
209280
'inputspec.{0}_white_K'.format(hemi))])])
210281

211282

212-
# Add more outputs to outputspec
283+
# Add more outputs to outputspec
213284
outputs = ar1_outputs + ar2_outputs + ar3_outputs
214285
outputspec = pe.Node(niu.IdentityInterface(fields=outputs, mandatory_inputs=True),
215286
name="outputspec")
@@ -401,14 +472,48 @@ def getDSTransformPath(subjects_dir, subject_id):
401472
('rh_table', 'label.@rh_table'),
402473
('rh_color', 'label.@rh_color'),
403474
('rh_thresh_table', 'label.@rh_thresh_table'),
404-
('rh_thresh_color', 'label.@rh_thresh_color')
475+
('rh_thresh_color', 'label.@rh_thresh_color'),
476+
('lh_BAMaps_labels', 'label.@lh_BAMaps_labels'),
477+
('lh_thresh_BAMaps_labels', 'label.@lh_thresh_BAMaps_labels'),
478+
('rh_BAMaps_labels', 'label.@rh_BAMaps_labels'),
479+
('rh_thresh_BAMaps_labels', 'label.@rh_thresh_BAMaps_labels'),
480+
('lh_BAMaps_annotation',
481+
'label.@lh_BAMaps_annotation'),
482+
('lh_thresh_BAMaps_annotation',
483+
'label.@lh_thresh_BAMaps_annotation'),
484+
('rh_BAMaps_annotation',
485+
'label.@rh_BAMaps_annotation'),
486+
('rh_thresh_BAMaps_annotation',
487+
'label.@rh_thresh_BAMaps_annotation'),
405488
]),
406489
])
407490

491+
# compeltion node
492+
# since recon-all outputs so many files a completion node is added
493+
# that will output the subject_id once the workflow has completed
494+
def completemethod(datasinked_files, subject_id):
495+
print("recon-all has finished executing for subject: {0}".format(subject_id))
496+
return subject_id
497+
498+
completion = pe.Node(niu.Function(['datasinked_files', 'subject_id'],
499+
['subject_id'],
500+
completemethod),
501+
name="Completion")
502+
503+
# create a special identity interface for outputing the subject_id
504+
505+
postds_outputspec = pe.Node(niu.IdentityInterface(['subject_id']),
506+
name="postdatasink_outputspec")
507+
508+
reconall.connect([(datasink, completion, [('out_file', 'datasinked_files')]),
509+
(inputspec, completion, [('subject_id', 'subject_id')]),
510+
(completion, postds_outputspec, [('subject_id', 'subject_id')])])
511+
512+
408513
#### Workflow additions go here
409-
if defaultconfig['recoding_file']:
514+
if recoding_file:
410515
from utils import create_recoding_wf
411-
recode = create_recoding_wf(defaultconfig['recoding_file'])
516+
recode = create_recoding_wf(recoding_file)
412517
reconall.connect([(ar3_wf, recode, [('outputspec.aseg', 'inputspec.labelmap')]),
413518
(recode, outputspec, [('outputspec.recodedlabelmap', 'recoded_labelmap')])])
414519

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