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‎.circleci/config.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -778,7 +778,7 @@ workflows:
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- get_regression_data
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filters:
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branches:
781-
ignore:
781+
ignore:
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- /docs?\/.*/
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- /ds005\/.*/
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- /ds054\/.*/

‎docs/workflows.rst

Lines changed: 59 additions & 56 deletions
Original file line numberDiff line numberDiff line change
@@ -19,38 +19,39 @@ is presented below:
1919
:simple_form: yes
2020

2121
from fmriprep.workflows.base import init_single_subject_wf
22-
wf = init_single_subject_wf(subject_id='test',
23-
name='single_subject_wf',
24-
task_id='',
25-
longitudinal=False,
26-
t2s_coreg=False,
27-
omp_nthreads=1,
28-
freesurfer=True,
29-
reportlets_dir='.',
30-
output_dir='.',
31-
bids_dir='.',
32-
skull_strip_template='OASIS',
33-
skull_strip_fixed_seed=False,
34-
template='MNI152NLin2009cAsym',
35-
output_spaces=['T1w', 'fsnative',
36-
'template', 'fsaverage5'],
37-
medial_surface_nan=False,
38-
cifti_output=False,
39-
ignore=[],
40-
debug=False,
41-
low_mem=False,
42-
anat_only=False,
43-
hires=True,
44-
use_bbr=True,
45-
bold2t1w_dof=9,
46-
fmap_bspline=False,
47-
fmap_demean=True,
48-
use_syn=True,
49-
force_syn=True,
50-
template_out_grid='native',
51-
use_aroma=False,
52-
aroma_melodic_dim=None,
53-
ignore_aroma_err=False)
22+
wf = init_single_subject_wf(
23+
subject_id='test',
24+
name='single_subject_wf',
25+
task_id='',
26+
longitudinal=False,
27+
t2s_coreg=False,
28+
omp_nthreads=1,
29+
freesurfer=True,
30+
reportlets_dir='.',
31+
output_dir='.',
32+
bids_dir='.',
33+
skull_strip_template='OASIS',
34+
skull_strip_fixed_seed=False,
35+
template='MNI152NLin2009cAsym',
36+
output_spaces=['T1w', 'fsnative', 'template', 'fsaverage5'],
37+
medial_surface_nan=False,
38+
cifti_output=False,
39+
ignore=[],
40+
debug=False,
41+
low_mem=False,
42+
anat_only=False,
43+
hires=True,
44+
use_bbr=True,
45+
bold2t1w_dof=9,
46+
fmap_bspline=False,
47+
fmap_demean=True,
48+
use_syn=True,
49+
force_syn=True,
50+
template_out_grid='native',
51+
use_aroma=False,
52+
aroma_melodic_dim=None,
53+
ignore_aroma_err=False,
54+
)
5455

5556

5657
T1w/T2w preprocessing
@@ -248,30 +249,32 @@ BOLD preprocessing
248249
:simple_form: yes
249250

250251
from fmriprep.workflows.bold import init_func_preproc_wf
251-
wf = init_func_preproc_wf('/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
252-
omp_nthreads=1,
253-
ignore=[],
254-
freesurfer=True,
255-
reportlets_dir='.',
256-
output_dir='.',
257-
template='MNI152NLin2009cAsym',
258-
output_spaces=['T1w', 'fsnative',
259-
'template', 'fsaverage5'],
260-
medial_surface_nan=False,
261-
cifti_output=False,
262-
debug=False,
263-
low_mem=False,
264-
use_bbr=True,
265-
t2s_coreg=False,
266-
bold2t1w_dof=9,
267-
fmap_bspline=True,
268-
fmap_demean=True,
269-
use_syn=True,
270-
force_syn=True,
271-
template_out_grid='native',
272-
use_aroma=False,
273-
aroma_melodic_dim=None,
274-
ignore_aroma_err=False)
252+
wf = init_func_preproc_wf(
253+
'/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
254+
omp_nthreads=1,
255+
ignore=[],
256+
freesurfer=True,
257+
reportlets_dir='.',
258+
output_dir='.',
259+
template='MNI152NLin2009cAsym',
260+
output_spaces=['T1w', 'fsnative',
261+
'template', 'fsaverage5'],
262+
medial_surface_nan=False,
263+
cifti_output=False,
264+
debug=False,
265+
low_mem=False,
266+
use_bbr=True,
267+
t2s_coreg=False,
268+
bold2t1w_dof=9,
269+
fmap_bspline=True,
270+
fmap_demean=True,
271+
use_syn=True,
272+
force_syn=True,
273+
template_out_grid='native',
274+
use_aroma=False,
275+
aroma_melodic_dim=None,
276+
ignore_aroma_err=False,
277+
)
275278

276279
Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is
277280
split into multiple sub-workflows described below.

‎fmriprep/workflows/base.py

Lines changed: 33 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -177,37 +177,39 @@ def init_fmriprep_wf(subject_list, task_id, run_uuid, work_dir, output_dir, bids
177177

178178
reportlets_dir = os.path.join(work_dir, 'reportlets')
179179
for subject_id in subject_list:
180-
single_subject_wf = init_single_subject_wf(subject_id=subject_id,
181-
task_id=task_id,
182-
name="single_subject_" + subject_id + "_wf",
183-
reportlets_dir=reportlets_dir,
184-
output_dir=output_dir,
185-
bids_dir=bids_dir,
186-
ignore=ignore,
187-
debug=debug,
188-
low_mem=low_mem,
189-
anat_only=anat_only,
190-
longitudinal=longitudinal,
191-
t2s_coreg=t2s_coreg,
192-
omp_nthreads=omp_nthreads,
193-
skull_strip_template=skull_strip_template,
194-
skull_strip_fixed_seed=skull_strip_fixed_seed,
195-
freesurfer=freesurfer,
196-
output_spaces=output_spaces,
197-
template=template,
198-
medial_surface_nan=medial_surface_nan,
199-
cifti_output=cifti_output,
200-
hires=hires,
201-
use_bbr=use_bbr,
202-
bold2t1w_dof=bold2t1w_dof,
203-
fmap_bspline=fmap_bspline,
204-
fmap_demean=fmap_demean,
205-
use_syn=use_syn,
206-
force_syn=force_syn,
207-
template_out_grid=template_out_grid,
208-
use_aroma=use_aroma,
209-
aroma_melodic_dim=aroma_melodic_dim,
210-
ignore_aroma_err=ignore_aroma_err)
180+
single_subject_wf = init_single_subject_wf(
181+
subject_id=subject_id,
182+
task_id=task_id,
183+
name="single_subject_" + subject_id + "_wf",
184+
reportlets_dir=reportlets_dir,
185+
output_dir=output_dir,
186+
bids_dir=bids_dir,
187+
ignore=ignore,
188+
debug=debug,
189+
low_mem=low_mem,
190+
anat_only=anat_only,
191+
longitudinal=longitudinal,
192+
t2s_coreg=t2s_coreg,
193+
omp_nthreads=omp_nthreads,
194+
skull_strip_template=skull_strip_template,
195+
skull_strip_fixed_seed=skull_strip_fixed_seed,
196+
freesurfer=freesurfer,
197+
output_spaces=output_spaces,
198+
template=template,
199+
medial_surface_nan=medial_surface_nan,
200+
cifti_output=cifti_output,
201+
hires=hires,
202+
use_bbr=use_bbr,
203+
bold2t1w_dof=bold2t1w_dof,
204+
fmap_bspline=fmap_bspline,
205+
fmap_demean=fmap_demean,
206+
use_syn=use_syn,
207+
force_syn=force_syn,
208+
template_out_grid=template_out_grid,
209+
use_aroma=use_aroma,
210+
aroma_melodic_dim=aroma_melodic_dim,
211+
ignore_aroma_err=ignore_aroma_err,
212+
)
211213

212214
single_subject_wf.config['execution']['crashdump_dir'] = (
213215
os.path.join(output_dir, "fmriprep", "sub-" + subject_id, 'log', run_uuid)

‎fmriprep/workflows/bold/stc.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -59,7 +59,7 @@ def init_bold_stc_wf(metadata, name='bold_stc_wf'):
5959
workflow.__desc__ = """\
6060
BOLD runs were slice-time corrected using `3dTshift` from
6161
AFNI {afni_ver} [@afni, RRID:SCR_005927].
62-
""".format(afni_ver=''.join(list(afni.TShift().version or '<ver>')))
62+
""".format(afni_ver=''.join(['%02d' % v for v in afni.Info().version() or []]))
6363
inputnode = pe.Node(niu.IdentityInterface(fields=['bold_file', 'skip_vols']), name='inputnode')
6464
outputnode = pe.Node(niu.IdentityInterface(fields=['stc_file']), name='outputnode')
6565

‎fmriprep/workflows/fieldmap/pepolar.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -105,7 +105,7 @@ def init_pepolar_unwarp_wf(bold_meta, epi_fmaps, omp_nthreads=1,
105105
A deformation field to correct for susceptibility distortions was estimated
106106
based on two echo-planar imaging (EPI) references with opposing phase-encoding
107107
directions, using `3dQwarp` @afni (AFNI {afni_ver}).
108-
""".format(afni_ver=''.join(list(afni.QwarpPlusMinus().version or '<ver>')))
108+
""".format(afni_ver=''.join(['%02d' % v for v in afni.Info().version() or []]))
109109

110110
inputnode = pe.Node(niu.IdentityInterface(
111111
fields=['in_reference', 'in_reference_brain', 'in_mask']), name='inputnode')

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