def tourette_reconall(population, data_dir, freesurfer_dir):
for subject in population:
#subject = population[subject_index]
print '========================================================================================'
print ' Runnning FREESURFER reconall on subject %s' % subject
print '========================================================================================'
brain = os.path.join(data_dir, subject, 'NIFTI', 'MP2RAGE_BRAIN.nii')
if os.path.isfile(brain):
if os.path.isfile(
os.path.join(freesurfer_dir, subject, 'mri',
'aparc.a2009s+aseg.mgz')):
print 'Brain already segmented......... moving on'
print 'check data here ---> %s' % (os.path.join(
freesurfer_dir, subject))
else:
fs_subdir = os.path.join(freesurfer_dir, subject)
print 'recon all not complete.. deleting incomplete fs_subdir'
os.system('rm -rf %s' % fs_subdir)
print 'Running recon-all'
'========================= '
' Freesurfer Reconall '
'========================= '
autorecon1 = fs.ReconAll()
autorecon1.plugin_args = {
'submit_specs': 'request_memory = 4000'
}
autorecon1.inputs.T1_files = brain
autorecon1.inputs.directive = "autorecon1"
autorecon1.inputs.args = "-noskullstrip"
#####autorecon1._interface._can_resume = False
autorecon1.inputs.subject_id = subject
autorecon1.inputs.subjects_dir = freesurfer_dir
autorecon1.run()
os.symlink(
os.path.join(freesurfer_dir, subject, "mri", "T1.mgz"),
os.path.join(freesurfer_dir, subject, "mri",
"brainmask.auto.mgz"))
os.symlink(
os.path.join(freesurfer_dir, subject, "mri",
"brainmask.auto.mgz"),
os.path.join(freesurfer_dir, subject, "mri",
"brainmask.mgz"))
autorecon_resume = fs.ReconAll()
autorecon_resume.plugin_args = {
'submit_specs': 'request_memory = 4000'
}
autorecon_resume.inputs.args = "-no-isrunning"
autorecon_resume.inputs.subject_id = subject
autorecon_resume.inputs.subjects_dir = freesurfer_dir
autorecon_resume.run()
else:
print 'Deskull brain before and then come back'
raise ValueError(
'MP2RAGE_BRAIN.nii file for subject %s does not exist')
def make_freesurfer(self):
# Ref: http://nipype.readthedocs.io/en/1.0.4/interfaces/generated/interfaces.freesurfer/preprocess.html#reconall
fs_recon1 = Node(interface=fs.ReconAll(directive='autorecon1',
mris_inflate='-n 15',
hires=True,
mprage=True,
openmp=self.omp_nthreads),
name='fs_recon1',
n_procs=self.omp_nthreads)
fs_mriconv = Node(interface=fs.MRIConvert(out_type='mgz'),
name='fs_mriconv')
fs_vol2vol = Node(interface=fs.ApplyVolTransform(mni_152_reg=True),
name='fs_vol2vol')
fs_mrimask = Node(interface=fs.ApplyMask(), name='fs_mrimask')
fs_recon2 = Node(interface=fs.ReconAll(directive='autorecon2',
hires=True,
mprage=True,
hippocampal_subfields_T1=False,
openmp=self.omp_nthreads),
name='fs_recon2',
n_procs=self.omp_nthreads)
fs_recon3 = Node(interface=fs.ReconAll(directive='autorecon3',
hires=True,
mprage=True,
hippocampal_subfields_T1=False,
openmp=self.omp_nthreads),
name='fs_recon3',
n_procs=self.omp_nthreads)
copy_brainmask = Node(Function(['in_file', 'fs_dir'], ['fs_dir'],
self.copy_mask),
name='copy_brainmask')
segment_hp = Node(interface=SegmentHA_T1(), name='segment_hp')
freesurfer = Workflow(name='freesurfer', base_dir=self.temp_dir)
freesurfer.connect(fs_recon1, 'T1', fs_vol2vol, 'target_file')
freesurfer.connect(fs_mriconv, 'out_file', fs_vol2vol, 'source_file')
freesurfer.connect(fs_recon1, 'T1', fs_mrimask, 'in_file')
freesurfer.connect(fs_vol2vol, 'transformed_file', fs_mrimask,
'mask_file')
freesurfer.connect(fs_mrimask, 'out_file', copy_brainmask, 'in_file')
freesurfer.connect(fs_recon1, 'subjects_dir', copy_brainmask, 'fs_dir')
freesurfer.connect(copy_brainmask, 'fs_dir', fs_recon2, 'subjects_dir')
freesurfer.connect(fs_recon2, 'subjects_dir', fs_recon3,
'subjects_dir')
freesurfer.connect(fs_recon3, 'subjects_dir', segment_hp,
'subjects_dir')
return freesurfer
def _generate_segment(self):
if not isdefined(self.inputs.subjects_dir):
freesurfer_status = "Not run"
else:
recon = fs.ReconAll(
subjects_dir=self.inputs.subjects_dir,
subject_id=self.inputs.subject_id,
T1_files=self.inputs.t1w,
flags="-noskullstrip",
)
if recon.cmdline.startswith("echo"):
freesurfer_status = "Pre-existing directory"
else:
freesurfer_status = "Run by sMRIPrep"
t2w_seg = ""
if self.inputs.t2w:
t2w_seg = "(+ {:d} T2-weighted)".format(len(self.inputs.t2w))
output_spaces = self.inputs.output_spaces
if not isdefined(output_spaces):
output_spaces = "<none given>"
else:
output_spaces = ", ".join(output_spaces)
return SUBJECT_TEMPLATE.format(
subject_id=self.inputs.subject_id,
n_t1s=len(self.inputs.t1w),
t2w=t2w_seg,
output_spaces=output_spaces,
freesurfer_status=freesurfer_status,
)
def _generate_segment(self):
if isdefined(self.inputs.template):
template = "\t\t<li>Volume standard spaces: {}</li>\n".format(
', '.join(self.inputs.template) if isinstance(
self.inputs.template, list) else self.inputs.template)
if not isdefined(self.inputs.subjects_dir):
freesurfer_status = 'Not run'
else:
recon = fs.ReconAll(subjects_dir=self.inputs.subjects_dir,
subject_id=self.inputs.subject_id,
T1_files=self.inputs.t1w,
flags='-noskullstrip')
if recon.cmdline.startswith('echo'):
freesurfer_status = 'Pre-existing directory'
else:
freesurfer_status = 'Run by sMRIPrep'
t2w_seg = ''
if self.inputs.t2w:
t2w_seg = '(+ {:d} T2-weighted)'.format(len(self.inputs.t2w))
return SUBJECT_TEMPLATE.format(subject_id=self.inputs.subject_id,
n_t1s=len(self.inputs.t1w),
t2w=t2w_seg,
template=template,
fs_spaces=', '.join(
self.inputs.fs_spaces),
freesurfer_status=freesurfer_status)
def create_reconall_pipeline(name='reconall'):
reconall=Workflow(name='reconall')
#inputnode
inputnode=Node(util.IdentityInterface(fields=['anat',
'fs_subjects_dir',
'fs_subject_id'
]),
name='inputnode')
outputnode=Node(util.IdentityInterface(fields=['fs_subjects_dir',
'fs_subject_id']),
name='outputnode')
def rename_subject_for_fu(input_id):
output_id=input_id+"_fu"
return output_id
#modify subject name so it can be saved in the same folder as other LIFE- freesurfer data
rename=Node(util.Function(input_names=['input_id'],
output_names=['output_id'],
function = rename_subject_for_fu), name="rename")
# run reconall
recon_all = Node(fs.ReconAll(args='-all -hippo-subfields -no-isrunning', openmp=24), #FS version 6.0: -hippocampal-subfields-T1, version 5.3.. -hippo-subfields
name="recon_all")
#recon_all.inputs.directive= 'autorecon2-wm' # -autorecon3
recon_all.plugin_args={'submit_specs': 'request_memory = 9000'}
reconall.connect([
(inputnode, rename, [('fs_subject_id', 'input_id')]),
(rename, recon_all, [('output_id', 'subject_id')]),
(inputnode, recon_all, [('fs_subjects_dir', 'subjects_dir'),
('anat', 'T1_files')]),
(recon_all, outputnode, [('subject_id', 'fs_subject_id'),
('subjects_dir', 'fs_subjects_dir')])
])
return reconall
def create_reconall_pipeline(name='reconall_wf'):
reconall_wf = Workflow(name='reconall_wf')
#inputnode
inputnode = Node(util.IdentityInterface(
fields=['anat', 'fs_subjects_dir', 'fs_subject_id']),
name='inputnode')
outputnode = Node(
util.IdentityInterface(fields=['fs_subjects_dir', 'fs_subject_id']),
name='outputnode')
# run reconall
reconall = Node(
fs.ReconAll(args='-all -no-isrunning',
openmp=8), #subfield segmentation after recon-all
name="reconall")
#recon_all.inputs.directive= 'autorecon2-wm' # -autorecon3
reconall_wf.plugin_args = {'submit_specs': 'request_memory = 9000'}
reconall_wf.connect([
(inputnode, reconall, [('fs_subject_id', 'subject_id')]),
(inputnode, reconall, [('fs_subjects_dir', 'subjects_dir'),
('anat', 'T1_files')]),
(reconall, outputnode, [('subject_id', 'fs_subject_id'),
('subjects_dir', 'fs_subjects_dir')])
])
return reconall_wf
def _generate_segment(self):
if not isdefined(self.inputs.subjects_dir):
freesurfer_status = 'Not run'
else:
recon = fs.ReconAll(subjects_dir=self.inputs.subjects_dir,
subject_id=self.inputs.subject_id,
T1_files=self.inputs.t1w,
flags='-noskullstrip')
if recon.cmdline.startswith('echo'):
freesurfer_status = 'Pre-existing directory'
else:
freesurfer_status = 'Run by dMRIPrep'
t2w_seg = ''
if self.inputs.t2w:
t2w_seg = '(+ {:d} T2-weighted)'.format(len(self.inputs.t2w))
dwi_files = self.inputs.dwi if isdefined(self.inputs.dwi) else []
dwi_files = [s[0] if isinstance(s, list) else s for s in dwi_files]
return SUBJECT_TEMPLATE.format(
subject_id=self.inputs.subject_id,
n_t1s=len(self.inputs.t1w),
t2w=t2w_seg,
n_dwi=len(dwi_files),
std_spaces=', '.join(self.inputs.std_spaces),
nstd_spaces=', '.join(self.inputs.nstd_spaces),
freesurfer_status=freesurfer_status)
def create_reconall_pipeline(name='reconall'):
reconall = Workflow(name='reconall')
#inputnode
inputnode = Node(util.IdentityInterface(
fields=['anat', 'fs_subjects_dir', 'fs_subject_id']),
name='inputnode')
outputnode = Node(
util.IdentityInterface(fields=['fs_subjects_dir', 'fs_subject_id']),
name='outputnode')
# run reconall
recon_all = Node(fs.ReconAll(args='-nuiterations 7 -no-isrunning'),
name="recon_all")
recon_all.plugin_args = {'submit_specs': 'request_memory = 9000'}
# function to replace / in subject id string with a _
def sub_id(sub_id):
return sub_id.replace('/', '_')
reconall.connect([
(inputnode, recon_all, [('fs_subjects_dir', 'subjects_dir'),
('anat', 'T1_files'),
(('fs_subject_id', sub_id), 'subject_id')]),
(recon_all, outputnode, [('subject_id', 'fs_subject_id'),
('subjects_dir', 'fs_subjects_dir')])
])
return reconall
def create_align_to_anatomy_workflow(name='align_to_anatomy',
format_string='inplane_to_anatomy'):
align_to_anatomy = pe.Workflow(name=name)
inputs = pe.Node(interface=util.IdentityInterface(
fields=['inplane_file', 'anatomy_file']),
name='inputs')
strip = pe.Node(interface=fs.ReconAll(),
name='strip') #FIXME: reconall interface barfs if rerun
strip.inputs.directive = 'autorecon1'
strip.inputs.flags = '-nowsgcaatlas'
register = pe.Node(interface=fs.RobustRegister(), name='register')
register.inputs.auto_sens = True
#register.inputs.init_orient = True #FIXME: disabled due to bug in binary
convert_xfm = pe.Node(interface=nmutil.LtaToXfm(), name='convert_xfm')
rename_xfm = pe.Node(interface=util.Rename(format_string),
name='rename_xfm')
rename_xfm.inputs.keep_ext = True
outputs = pe.Node(
interface=util.IdentityInterface(fields=['xfm_file', 'strip_file']),
name='outputs')
align_to_anatomy.connect(inputs, 'inplane_file', strip, 'T1_files')
align_to_anatomy.connect(strip, 'brainmask', register, 'source_file')
align_to_anatomy.connect(inputs, 'anatomy_file', register, 'target_file')
align_to_anatomy.connect(register, 'out_reg_file', convert_xfm, 'in_file')
align_to_anatomy.connect(convert_xfm, 'out_file', rename_xfm, 'in_file')
align_to_anatomy.connect(rename_xfm, 'out_file', outputs, 'xfm_file')
align_to_anatomy.connect(strip, 'brainmask', outputs, 'strip_file')
return align_to_anatomy
def create_reconall_pipeline(name='reconall'):
reconall = Workflow(name='reconall')
#inputnode
inputnode = Node(util.IdentityInterface(
fields=['anat', 'fs_subjects_dir', 'fs_subject_id']),
name='inputnode')
outputnode = Node(
util.IdentityInterface(fields=['fs_subjects_dir', 'fs_subject_id']),
name='outputnode')
# run reconall
recon_all = Node(
fs.ReconAll(
args='-all -hippo-subfields -no-isrunning'
), #for RSV152 took out s because of preprocessing with version 6.0
name="recon_all")
#recon_all.inputs.directive= 'autorecon2-wm' # -autorecon3
recon_all.plugin_args = {'submit_specs': 'request_memory = 9000'}
# function to replace / in subject id string with a _
def sub_id(sub_id):
return sub_id.replace('/', '_')
reconall.connect([
(inputnode, recon_all, [('fs_subjects_dir', 'subjects_dir'),
('anat', 'T1_files'),
(('fs_subject_id', sub_id), 'subject_id')]),
(recon_all, outputnode, [('subject_id', 'fs_subject_id'),
('subjects_dir', 'fs_subjects_dir')])
])
return reconall
def _generate_segment(self):
if not isdefined(self.inputs.subjects_dir):
freesurfer_status = 'Not run'
else:
recon = fs.ReconAll(subjects_dir=self.inputs.subjects_dir,
subject_id=self.inputs.subject_id,
T1_files=self.inputs.t1w,
flags='-noskullstrip')
if recon.cmdline.startswith('echo'):
freesurfer_status = 'Pre-existing directory'
else:
freesurfer_status = 'Run by qsiprep'
output_spaces = [
self.inputs.template if space == 'template' else space
for space in self.inputs.output_spaces
]
t2w_seg = ''
if self.inputs.t2w:
t2w_seg = '(+ {:d} T2-weighted)'.format(len(self.inputs.t2w))
# Add text for how the dwis are grouped
n_dwis = 0
n_outputs = 0
groupings = ''
if isdefined(self.inputs.dwi_groupings):
for output_fname, group_info in self.inputs.dwi_groupings.items():
n_outputs += 1
files_desc = []
files_desc.append(
'\t\t\t<li>Scan group: %s (PE Dir %s)</li><ul>' %
(output_fname, group_info['dwi_series_pedir']))
files_desc.append('\t\t\t\t<li>DWI Files: </li>')
for dwi_file in group_info['dwi_series']:
files_desc.append("\t\t\t\t\t<li> %s </li>" % dwi_file)
n_dwis += 1
fieldmap_type = group_info['fieldmap_info']['suffix']
if fieldmap_type is not None:
files_desc.append('\t\t\t\t<li>Fieldmap type: %s </li>' %
fieldmap_type)
for key, value in group_info['fieldmap_info'].items():
files_desc.append("\t\t\t\t\t<li> %s: %s </li>" %
(key, str(value)))
n_dwis += 1
files_desc.append("</ul>")
groupings += GROUPING_TEMPLATE.format(
output_name=output_fname,
input_files='\n'.join(files_desc))
return SUBJECT_TEMPLATE.format(subject_id=self.inputs.subject_id,
n_t1s=len(self.inputs.t1w),
t2w=t2w_seg,
n_dwis=n_dwis,
n_outputs=n_outputs,
groupings=groupings,
output_spaces=', '.join(output_spaces),
freesurfer_status=freesurfer_status)
def _generate_segment(self):
BIDS_NAME = re.compile(r'^(.*\/)?'
'(?P<subject_id>sub-[a-zA-Z0-9]+)'
'(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
'(_(?P<task_id>task-[a-zA-Z0-9]+))?'
'(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'
'(_(?P<rec_id>rec-[a-zA-Z0-9]+))?'
'(_(?P<run_id>run-[a-zA-Z0-9]+))?')
if not isdefined(self.inputs.subjects_dir):
freesurfer_status = 'Not run'
else:
recon = fs.ReconAll(subjects_dir=self.inputs.subjects_dir,
subject_id=self.inputs.subject_id,
T1_files=self.inputs.t1w,
flags='-noskullstrip')
if recon.cmdline.startswith('echo'):
freesurfer_status = 'Pre-existing directory'
else:
freesurfer_status = 'Run by fMRIPrep'
t2w_seg = ''
if self.inputs.t2w:
t2w_seg = '(+ {:d} T2-weighted)'.format(len(self.inputs.t2w))
# Add list of tasks with number of runs
bold_series = self.inputs.bold if isdefined(self.inputs.bold) else []
bold_series = [s[0] if isinstance(s, list) else s for s in bold_series]
counts = Counter(
BIDS_NAME.search(series).groupdict()['task_id'][5:]
for series in bold_series)
tasks = ''
if counts:
header = '\t\t<ul class="elem-desc">'
footer = '\t\t</ul>'
lines = [
'\t\t\t<li>Task: {task_id} ({n_runs:d} run{s})</li>'.format(
task_id=task_id,
n_runs=n_runs,
s='' if n_runs == 1 else 's')
for task_id, n_runs in sorted(counts.items())
]
tasks = '\n'.join([header] + lines + [footer])
return SUBJECT_TEMPLATE.format(
subject_id=self.inputs.subject_id,
n_t1s=len(self.inputs.t1w),
t2w=t2w_seg,
n_bold=len(bold_series),
tasks=tasks,
std_spaces=', '.join(self.inputs.std_spaces),
nstd_spaces=', '.join(self.inputs.nstd_spaces),
freesurfer_status=freesurfer_status)
def create_workflow(self, flow, inputnode, outputnode):
if self.config.seg_tool == "Freesurfer":
# Converting to .mgz format
fs_mriconvert = pe.Node(interface=fs.MRIConvert(out_type="mgz",
out_file="T1.mgz"),
name="mgz_convert")
if self.config.make_isotropic:
fs_mriconvert.inputs.vox_size = (
self.config.isotropic_vox_size,
self.config.isotropic_vox_size,
self.config.isotropic_vox_size)
fs_mriconvert.inputs.resample_type = self.config.isotropic_interpolation
rename = pe.Node(util.Rename(), name="copy_orig")
orig_dir = os.path.join(self.config.freesurfer_subject_id, "mri",
"orig")
if not os.path.exists(orig_dir):
os.makedirs(orig_dir)
print "Folder not existing; %s created!" % orig_dir
rename.inputs.format_string = os.path.join(orig_dir, "001.mgz")
# ReconAll => named outputnode as we don't want to select a specific output....
fs_reconall = pe.Node(interface=fs.ReconAll(
flags='-no-isrunning -parallel -openmp {}'.format(
self.config.fs_number_of_cores)),
name="reconall")
fs_reconall.inputs.directive = 'all'
#fs_reconall.inputs.args = self.config.freesurfer_args
#fs_reconall.inputs.subjects_dir and fs_reconall.inputs.subject_id set in cmp/pipelines/diffusion/diffusion.py
fs_reconall.inputs.subjects_dir = self.config.freesurfer_subjects_dir
# fs_reconall.inputs.hippocampal_subfields_T1 = self.config.segment_hippocampal_subfields
# fs_reconall.inputs.brainstem = self.config.segment_brainstem
def isavailable(file):
print "T1 is available"
return file
flow.connect([
(inputnode, fs_mriconvert, [(('T1', isavailable), 'in_file')]),
(fs_mriconvert, rename, [('out_file', 'in_file')]),
(rename, fs_reconall, [(("out_file", extract_base_directory),
"subject_id")]),
(fs_reconall, outputnode, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
])
def test_reconall():
input_map = dict(
T1_files=dict(argstr='-i %s...', ),
args=dict(argstr='%s', ),
directive=dict(argstr='-%s', ),
environ=dict(),
flags=dict(argstr='%s', ),
hemi=dict(),
subject_id=dict(argstr='-subjid %s', ),
subjects_dir=dict(argstr='-sd %s', ),
)
instance = freesurfer.ReconAll()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(instance.inputs.traits()[key],
metakey), value, "key = %s" % key
def create_workflow(self, flow, inputnode, outputnode):
if self.config.seg_tool == "Freesurfer":
if self.config.use_existing_freesurfer_data == False:
# Converting to .mgz format
fs_mriconvert = pe.Node(interface=fs.MRIConvert(
out_type="mgz", out_file="T1.mgz"),
name="mgz_convert")
rename = pe.Node(util.Rename(), name="copy_orig")
orig_dir = os.path.join(self.config.freesurfer_subject_id,
"mri", "orig")
if not os.path.exists(orig_dir):
os.makedirs(orig_dir)
print "Folder not existing; %s created!" % orig_dir
rename.inputs.format_string = os.path.join(orig_dir, "001.mgz")
# ReconAll => named outputnode as we don't want to select a specific output....
fs_reconall = pe.Node(
interface=fs.ReconAll(flags='-no-isrunning'),
name="reconall")
fs_reconall.inputs.args = self.config.freesurfer_args
#fs_reconall.inputs.subjects_dir and fs_reconall.inputs.subject_id set in cmp/pipelines/diffusion/diffusion.py
fs_reconall.inputs.subjects_dir = self.config.freesurfer_subjects_dir
def isavailable(file):
print "T1 is available"
return file
flow.connect([
(inputnode, fs_mriconvert, [(('T1', isavailable),
'in_file')]),
(fs_mriconvert, rename, [('out_file', 'in_file')]),
(rename, fs_reconall,
[(("out_file", extract_base_directory), "subject_id")]),
(fs_reconall, outputnode, [('subjects_dir',
'subjects_dir'),
('subject_id', 'subject_id')]),
])
else:
outputnode.inputs.subjects_dir = self.config.freesurfer_subjects_dir
outputnode.inputs.subject_id = self.config.freesurfer_subject_id
elif self.config.seg_tool == "Custom segmentation":
outputnode.inputs.custom_wm_mask = self.config.white_matter_mask
def _generate_segment(self):
if not isdefined(self.inputs.subjects_dir):
freesurfer_status = 'Not run'
else:
recon = fs.ReconAll(subjects_dir=self.inputs.subjects_dir,
subject_id=self.inputs.subject_id,
T1_files=self.inputs.t1w,
flags='-noskullstrip')
if recon.cmdline.startswith('echo'):
freesurfer_status = 'Pre-existing directory'
else:
freesurfer_status = 'Run by sMRIPrep'
t2w_seg = ''
if self.inputs.t2w:
t2w_seg = '(+ {:d} T2-weighted)'.format(len(self.inputs.t2w))
return SUBJECT_TEMPLATE.format(subject_id=self.inputs.subject_id,
n_t1s=len(self.inputs.t1w),
t2w=t2w_seg,
output_spaces=', '.join(self.inputs.output_spaces),
freesurfer_status=freesurfer_status)
def nipype_reconall(t1path, t2path=None):
splitpath = t1path.split(os.sep)
# Reorientation using FSL
reodir = os.path.join(BIDS_DATA_DIR, "derivatives",
"reorient_{0}".format(splitpath[-3]), splitpath[-4])
if not os.path.isdir(reodir):
os.makedirs(reodir)
reopath = []
for path in (t1path, t2path):
if path is not None:
reopath.append(os.path.join(reodir, os.path.basename(path)))
else:
reopath.append(None)
continue
reorient = fsl.Reorient2Std(in_file=path, out_file=reopath[-1])
if PROCESS:
reorient.run()
t1path, t2path = reopath
# Segmentation using FreeSurfer
fsdir = os.path.join(BIDS_DATA_DIR, "derivatives",
"freesurfer_{0}".format(splitpath[-3]))
if not os.path.isdir(fsdir):
os.makedirs(fsdir)
reconall = freesurfer.ReconAll(subject_id=splitpath[-4],
directive="all",
subjects_dir=fsdir,
T1_files=t1path)
if t2path is not None:
reconall.inputs.T2_file = t2path
reconall.inputs.use_T2 = True
if PROCESS:
reconall.run()
return reconall.cmdline
def cortical_recon(self, filepath=None):
if filepath == None:
filepath = self._data_dir
freesurfer.ReconAll(filepath)
def create_skullstripped_recon_flow(name="skullstripped_recon_all"):
"""Performs recon-all on voulmes that are already skull stripped.
FreeSurfer failes to perform skullstrippig on some volumes (especially
MP2RAGE). This can be avoided by doing skullstripping before runnig recon-all
(using for example SPECTRE algorithm)
Example
-------
>>> from nipype.workflows.smri.freesurfer import create_skullstripped_recon_flow
>>> recon_flow = create_skullstripped_recon_flow()
>>> recon_flow.inputs.inputspec.subject_id = 'subj1'
>>> recon_flow.inputs.inputspec.T1_files = 'T1.nii.gz'
>>> recon_flow.run() # doctest: +SKIP
Inputs::
inputspec.T1_files : skullstripped T1_files (mandatory)
inputspec.subject_id : freesurfer subject id (optional)
inputspec.subjects_dir : freesurfer subjects directory (optional)
Outputs::
outputspec.subject_id : freesurfer subject id
outputspec.subjects_dir : freesurfer subjects directory
"""
wf = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['subject_id',
'subjects_dir',
'T1_files']),
name='inputspec')
autorecon1 = pe.Node(fs.ReconAll(), name="autorecon1")
autorecon1.plugin_args={'submit_specs': 'request_memory = 2500'}
autorecon1.inputs.directive = "autorecon1"
autorecon1.inputs.args = "-noskullstrip"
autorecon1._interface._can_resume = False
wf.connect(inputnode, "T1_files", autorecon1, "T1_files")
wf.connect(inputnode, "subjects_dir", autorecon1, "subjects_dir")
wf.connect(inputnode, "subject_id", autorecon1, "subject_id")
def link_masks(subjects_dir, subject_id):
import os
os.symlink(os.path.join(subjects_dir, subject_id, "mri", "T1.mgz"),
os.path.join(subjects_dir, subject_id, "mri", "brainmask.auto.mgz"))
os.symlink(os.path.join(subjects_dir, subject_id, "mri", "brainmask.auto.mgz"),
os.path.join(subjects_dir, subject_id, "mri", "brainmask.mgz"))
return subjects_dir, subject_id
masks = pe.Node(niu.Function(input_names=['subjects_dir', 'subject_id'],
output_names=['subjects_dir', 'subject_id'],
function=link_masks), name="link_masks")
wf.connect(autorecon1, "subjects_dir", masks, "subjects_dir")
wf.connect(autorecon1, "subject_id", masks, "subject_id")
autorecon_resume = pe.Node(fs.ReconAll(), name="autorecon_resume")
autorecon_resume.plugin_args={'submit_specs': 'request_memory = 2500'}
autorecon_resume.inputs.args = "-no-isrunning"
wf.connect(masks, "subjects_dir", autorecon_resume, "subjects_dir")
wf.connect(masks, "subject_id", autorecon_resume, "subject_id")
outputnode = pe.Node(niu.IdentityInterface(fields=['subject_id',
'subjects_dir']),
name='outputspec')
wf.connect(autorecon_resume, "subjects_dir", outputnode, "subjects_dir")
wf.connect(autorecon_resume, "subject_id", outputnode, "subject_id")
return wf
def create_workflow(self, flow, inputnode, outputnode):
"""Create the stage workflow.
Parameters
----------
flow : nipype.pipeline.engine.Workflow
The nipype.pipeline.engine.Workflow instance of the anatomical pipeline
inputnode : nipype.interfaces.utility.IdentityInterface
Identity interface describing the inputs of the segmentation stage
outputnode : nipype.interfaces.utility.IdentityInterface
Identity interface describing the outputs of the segmentation stage
"""
if self.config.seg_tool == "Freesurfer":
def correct_freesurfer_subjectid_path(path):
if os.path.exists('/output_dir') and '/output_dir' not in path:
subject_id = path.split(f"{__freesurfer_directory__}/")[-1]
path = os.path.abspath(f'/output_dir/{__freesurfer_directory__}/{subject_id}')
return path
def correct_freesurfer_subjects_path(path):
if os.path.exists('/output_dir') and '/output_dir' not in path:
path = os.path.abspath(f'/output_dir/{__freesurfer_directory__}')
return path
orig_dir = os.path.join(
correct_freesurfer_subjectid_path(self.config.freesurfer_subject_id), "mri", "orig"
)
print(f'INFO : orig_dir = {orig_dir}')
# Skip Freesurfer recon-all if 001.mgz exists which typically means it has been already run
self.config.use_existing_freesurfer_data = True if os.path.exists(orig_dir) else False
print(f'INFO : orig_dir exists? {self.config.use_existing_freesurfer_data}')
if self.config.use_existing_freesurfer_data is False:
# Converting to .mgz format
fs_mriconvert = pe.Node(
interface=fs.MRIConvert(out_type="mgz", out_file="T1.mgz"),
name="mgzConvert",
)
if self.config.make_isotropic:
fs_mriconvert.inputs.vox_size = (
self.config.isotropic_vox_size,
self.config.isotropic_vox_size,
self.config.isotropic_vox_size,
)
fs_mriconvert.inputs.resample_type = (
self.config.isotropic_interpolation
)
rename = pe.Node(Rename001(), name="copyOrig")
if not os.path.exists(orig_dir):
print(f'INFO : Create folder: {orig_dir}')
os.makedirs(orig_dir)
rename.inputs.format_string = os.path.join(orig_dir, "001.mgz")
if self.config.brain_mask_extraction_tool == "Freesurfer":
# ReconAll => named outputnode as we don't want to select a specific output....
fs_reconall = pe.Node(
interface=fs.ReconAll(
flags=f'-no-isrunning -parallel -openmp {self.config.number_of_threads}'
),
name="reconall",
)
fs_reconall.inputs.directive = "all"
fs_reconall.inputs.args = self.config.freesurfer_args
# fs_reconall.inputs.subjects_dir and fs_reconall.inputs.subject_id set
# in cmp/pipelines/diffusion/diffusion.py
fs_reconall.inputs.subjects_dir = (
correct_freesurfer_subjects_path(self.config.freesurfer_subjects_dir)
)
# fmt: off
flow.connect(
[
(inputnode, fs_mriconvert, [(("T1", isavailable), "in_file")]),
(fs_mriconvert, rename, [("out_file", "in_file")]),
(rename, fs_reconall, [(("out_file", extract_reconall_base_dir), "subject_id")]),
(fs_reconall, outputnode, [("subjects_dir", "subjects_dir"), ("subject_id", "subject_id")]),
]
)
# fmt: on
else:
# ReconAll => named outputnode as we don't want to select a specific output....
fs_autorecon1 = pe.Node(
interface=fs.ReconAll(
flags="-no-isrunning -parallel -openmp {}".format(
self.config.number_of_threads
)
),
name="autorecon1",
)
fs_autorecon1.inputs.directive = "autorecon1"
if self.config.brain_mask_extraction_tool == "ANTs":
fs_autorecon1.inputs.flags = (
"-no-isrunning -noskullstrip -parallel -openmp {}".format(
self.config.number_of_threads
)
)
fs_autorecon1.inputs.args = self.config.freesurfer_args
# fs_reconall.inputs.subjects_dir and fs_reconall.inputs.subject_id set
# in cmp/pipelines/diffusion/diffusion.py
fs_autorecon1.inputs.subjects_dir = (
correct_freesurfer_subjects_path(self.config.freesurfer_subjects_dir)
)
# fmt: off
flow.connect(
[
(inputnode, fs_mriconvert, [(("T1", isavailable), "in_file")]),
(fs_mriconvert, rename, [("out_file", "in_file")]),
(rename, fs_autorecon1, [(("out_file", extract_reconall_base_dir), "subject_id")]),
]
)
# fmt: on
fs_source = pe.Node(interface=FreeSurferSource(), name="fsSource")
fs_mriconvert_nu = pe.Node(
interface=fs.MRIConvert(out_type="niigz", out_file="nu.nii.gz"),
name="niigzConvert",
)
# fmt: off
flow.connect(
[
(fs_autorecon1, fs_source, [("subjects_dir", "subjects_dir"),
("subject_id", "subject_id")]),
(fs_source, fs_mriconvert_nu, [("nu", "in_file")]),
]
)
# fmt: on
fs_mriconvert_brainmask = pe.Node(
interface=fs.MRIConvert(
out_type="mgz", out_file="brainmask.mgz"
),
name="fsMriconvertBETbrainmask",
)
if self.config.brain_mask_extraction_tool == "BET":
fsl_bet = pe.Node(
interface=fsl.BET(
out_file="brain.nii.gz",
mask=True,
skull=True,
robust=True,
),
name="fsl_bet",
)
# fmt: off
flow.connect(
[
(fs_mriconvert_nu, fsl_bet, [("out_file", "in_file")]),
(fsl_bet, fs_mriconvert_brainmask, [("out_file", "in_file")]),
]
)
# fmt: on
elif self.config.brain_mask_extraction_tool == "ANTs":
ants_bet = pe.Node(
interface=ants.BrainExtraction(out_prefix="ants_bet_"),
name="antsBET",
)
ants_bet.inputs.brain_template = self.config.ants_templatefile
ants_bet.inputs.brain_probability_mask = (
self.config.ants_probmaskfile
)
ants_bet.inputs.extraction_registration_mask = (
self.config.ants_regmaskfile
)
ants_bet.inputs.num_threads = self.config.number_of_threads
# fmt: off
flow.connect(
[
(fs_mriconvert_nu, ants_bet, [("out_file", "anatomical_image")]),
(ants_bet, fs_mriconvert_brainmask, [("BrainExtractionBrain", "in_file")]),
]
)
# fmt: on
copy_brainmask_to_fs = pe.Node(
interface=copyBrainMaskToFreesurfer(), name="copyBrainmaskTofs"
)
# fmt: off
flow.connect(
[
(rename, copy_brainmask_to_fs, [(("out_file", extract_reconall_base_dir), "subject_dir")]),
(fs_mriconvert_brainmask, copy_brainmask_to_fs, [("out_file", "in_file")]),
]
)
# fmt: on
fs_reconall23 = pe.Node(
interface=fs.ReconAll(
flags="-no-isrunning -parallel -openmp {}".format(
self.config.number_of_threads
)
),
name="reconall23",
)
fs_reconall23.inputs.directive = "autorecon2"
fs_reconall23.inputs.args = self.config.freesurfer_args
fs_reconall23.inputs.flags = "-autorecon3"
fs_reconall23.inputs.subjects_dir = (
correct_freesurfer_subjects_path(self.config.freesurfer_subjects_dir)
)
# fmt: off
flow.connect(
[
(copy_brainmask_to_fs,fs_reconall23, [(("out_brainmask_file", get_freesurfer_subject_id), "subject_id")]),
(fs_reconall23, outputnode, [("subjects_dir", "subjects_dir"),
("subject_id", "subject_id")]),
]
)
# fmt: on
else:
outputnode.inputs.subjects_dir = correct_freesurfer_subjects_path(self.config.freesurfer_subjects_dir)
outputnode.inputs.subject_id = correct_freesurfer_subjectid_path(self.config.freesurfer_subject_id)
print(f'INFO : Found existing {os.path.join(orig_dir, "001.mgz")} -> Skip Freesurfer recon-all')
print(f' - outputnode.inputs.subjects_dir: {outputnode.inputs.subjects_dir}')
print(f' - outputnode.inputs.subject_id: {outputnode.inputs.subject_id}')
elif self.config.seg_tool == "Custom segmentation":
self.create_workflow_custom(flow, inputnode, outputnode)
preprocessing.connect(iter_fwhm, "fwhm", isotropic_voxel_smooth, "fwhm")
compute_mask = pe.Node(interface=nipy.ComputeMask(), name="compute_mask")
preprocessing.connect(realign, "mean_image", compute_mask, "mean_volume")
anisotropic_voxel_smooth = fsl_wf.create_susan_smooth(
name="anisotropic_voxel_smooth", separate_masks=False)
anisotropic_voxel_smooth.inputs.smooth.output_type = 'NIFTI'
preprocessing.connect(realign, "realigned_files", anisotropic_voxel_smooth,
"inputnode.in_files")
preprocessing.connect(iter_fwhm, "fwhm", anisotropic_voxel_smooth,
"inputnode.fwhm")
preprocessing.connect(compute_mask, "brain_mask", anisotropic_voxel_smooth,
'inputnode.mask_file')
recon_all = pe.Node(interface=fs.ReconAll(), name="recon_all")
surfregister = pe.Node(interface=fs.BBRegister(), name='surfregister')
surfregister.inputs.init = 'fsl'
surfregister.inputs.contrast_type = 't2'
preprocessing.connect(realign, 'mean_image', surfregister, 'source_file')
preprocessing.connect(recon_all, 'subject_id', surfregister, 'subject_id')
preprocessing.connect(recon_all, 'subjects_dir', surfregister, 'subjects_dir')
isotropic_surface_smooth = pe.MapNode(
interface=fs.Smooth(proj_frac_avg=(0, 1, 0.1)),
iterfield=['in_file'],
name="isotropic_surface_smooth")
preprocessing.connect(surfregister, 'out_reg_file', isotropic_surface_smooth,
'reg_file')
preprocessing.connect(realign, "realigned_files", isotropic_surface_smooth,
def reconall(subjfile, subjID=None, subjdir=None, runreconall=True):
"""
Carries out Freesurfer's reconall on T1 nifti file
WARNING: Reconall takes very long to run!!
http://nipy.sourceforge.net/nipype/users/examples/smri_freesurfer.html
Parameters
----------
subjfile: nifti file
Path to subject's T1 nifti file
subjID: string
optional name for subject's output folder
subjdir: string
The directory to where segmentation results should be saved. Defaults
to same directory as subjfile.
runreconall: boolean
If set to true, runs reconall, otherwise just converts assorted mgz
files to nii
"""
T1dir = os.path.dirname(subjfile)
filename = os.path.basename(subjfile)
# subject ID
if subjID == None:
m = re.search('(\w+?)_*_', subjfile)
subjID = m.group(0) + 'seg'
# Tell freesurfer what subjects directory to use
if subjdir == None:
subjdir = T1dir
fs.FSCommand.set_default_subjects_dir(subjdir)
segdir = subjdir + '/' + subjID + '/'
print('saving to ' + subjdir)
# check if file exists
if os.path.isfile(subjfile):
print('running recon-all on ' + filename)
else:
raise ValueError("File: %s does not exist!" % filename)
# check if nifti format
ext = filename.split('.')[1].lower()
if ext != "nii":
raise ValueError("File: %s is not a nifti file!" % filename)
wf = pe.Workflow(name="segment")
wf.base_dir = T1dir
if runreconall:
# run recon-all
reconall = pe.Node(interface=fs.ReconAll(), name='reconall')
reconall.inputs.subject_id = subjID
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = subjdir
reconall.inputs.T1_files = subjfile
wf.add_nodes([reconall])
result = wf.run()
# convert mgz to nii
wf2 = pe.Workflow(name="convertmgz")
wf2.base_dir = T1dir
convertmgz = pe.Node(interface=fs.MRIConvert(), name='convertmgz')
convertmgz.inputs.in_file = segdir + 'mri/aseg.auto.mgz'
convertmgz.inputs.out_orientation = 'LPS'
convertmgz.inputs.resample_type = 'nearest'
convertmgz.inputs.reslice_like = subjfile
convertmgz.inputs.out_file = segdir + subjID + '_aseg.nii.gz'
wf2.add_nodes([convertmgz])
result2 = wf2.run()
if runreconall:
return (result, result2)
else:
return (result2)
def create_surface_registration(wf_name='surface_registration'):
"""
Workflow to generate surface from anatomical data and register
the structural data to FreeSurfer anatomical and assign it
to a surface vertex.
Parameters
----------
wf_name : string
name of the workflow
Returns
-------
wflow : workflow object
workflow object
Notes
-----
`Source <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/timeseries/timeseries_analysis.py>`_
Workflow Inputs::
inputspec.rest : string (nifti file)
path to input functional data
inputspec.brain : string (nifti file)
path to skull stripped anatomical image
inputspec.recon_subjects : string
path to subjects directory
inputspec.subject_id : string
subject id
Workflow Outputs::
outputspec.reconall_subjects_dir : string
freesurfer subjects directory
outputspec.reconall_subjects_id : string
subject id for which anatomical data is taken
outputspec.out_reg_file : string
path to bbregister output registration file
outputspec.lh_surface_file : string (mgz file)
path to left hemisphere cortical surface file
outputspec.rh_surface_file : string (mgz file)
path to right hemisphere cortical surface file
Order of commands:
- Generate surfaces and rois of structural data from T1 anatomical Image using FreeSurfer's reconall . For details see `ReconAll <https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all>`_::
recon-all -all -subjid 0010001 -sd working_dir/SurfaceRegistration/anat_reconall
- Register input volume to the FreeSurfer anatomical using FreeSurfer's bbregister. The input is the output of the recon-all command. For details see `BBRegister <http://surfer.nmr.mgh.harvard.edu/fswiki/bbregister>`_::
bbregister --t2 --init -fsl --reg structural_bbreg_me.dat --mov structural.nii --s 0010001
- Assign values from a volume to each surface vertex using FreeSurfer's mri_vol2surf . For details see `mri_vol2surf <http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf>`_::
For left hemisphere
mri_vol2surf --mov structural.nii --reg structural_bbreg_me.dat --interp trilin --projfrac 0.5 --hemi lh --o surface_file.nii.gz
For right hemisphere
mri_vol2surf --mov structural.nii --reg structural_bbreg_me.dat --interp trilin --projfrac 0.5 --hemi rh --o surface_file.nii.gz
High Level Workflow Graph:
.. image:: ../images/surface_registration.dot.png
:width: 1000
Detailed Workflow Graph:
.. image:: ../images/surface_registration_detailed.dot.png
:width: 1000
Example
-------
>>> import CPAC.timeseries.timeseries_analysis as t
>>> wf = t.create_surface_registration()
>>> wf.inputs.inputspec.rest = '/home/data/sub001/rest.nii.gz'
>>> wf.inputs.inputspec.brain = '/home/data/sub001/anat.nii.gz'
>>> wf.inputs.inputspec.recon_subjects = '/home/data/working_dir/SurfaceRegistration/anat_reconall'
>>> wf.inputs.inputspec.subject_id = 'sub001'
>>> wf.base_dir = './'
>>> wf.run()
"""
wflow = pe.Workflow(name=wf_name)
inputNode = pe.Node(util.IdentityInterface(fields=['recon_subjects',
'brain',
'subject_id',
'rest']),
name='inputspec')
outputNode = pe.Node(util.IdentityInterface(fields=['reconall_subjects_dir',
'reconall_subjects_id',
'out_reg_file',
'lh_surface_file',
'rh_surface_file']),
name='outputspec')
reconall = pe.Node(interface=fs.ReconAll(),
name="reconall")
reconall.inputs.directive = 'all'
wflow.connect(inputNode, 'brain',
reconall, 'T1_files')
wflow.connect(inputNode, 'subject_id',
reconall, 'subject_id')
wflow.connect(inputNode, 'recon_subjects',
reconall, 'subjects_dir')
wflow.connect(reconall, 'subjects_dir',
outputNode, 'reconall_subjects_dir')
wflow.connect(reconall, 'subject_id',
outputNode, 'reconall_subjects_id')
bbregister = pe.Node(interface=fs.BBRegister(init='fsl',
contrast_type='t2',
registered_file=True,
out_fsl_file=True),
name='bbregister')
wflow.connect(inputNode, 'rest',
bbregister, 'source_file')
wflow.connect(reconall, 'subjects_dir',
bbregister, 'subjects_dir')
wflow.connect(reconall, 'subject_id',
bbregister, 'subject_id')
wflow.connect(bbregister, 'out_reg_file',
outputNode, 'out_reg_file')
sample_to_surface_lh = pe.Node(interface=fs.SampleToSurface(hemi="lh"),
name='sample_to_surface_lh')
sample_to_surface_lh.inputs.no_reshape = True
sample_to_surface_lh.inputs.interp_method = 'trilinear'
sample_to_surface_lh.inputs.sampling_method = "point"
sample_to_surface_lh.inputs.sampling_range = 0.5
sample_to_surface_lh.inputs.sampling_units = "frac"
wflow.connect(bbregister, 'out_reg_file',
sample_to_surface_lh, 'reg_file')
wflow.connect(inputNode, 'rest',
sample_to_surface_lh, 'source_file')
wflow.connect(sample_to_surface_lh, 'out_file',
outputNode, 'lh_surface_file')
sample_to_surface_rh = pe.Node(interface=fs.SampleToSurface(hemi="rh"),
name='sample_to_surface_rh')
sample_to_surface_rh.inputs.no_reshape = True
sample_to_surface_rh.inputs.interp_method = 'trilinear'
sample_to_surface_rh.inputs.sampling_method = "point"
sample_to_surface_rh.inputs.sampling_range = 0.5
sample_to_surface_rh.inputs.sampling_units = "frac"
wflow.connect(bbregister, 'out_reg_file',
sample_to_surface_rh, 'reg_file')
wflow.connect(inputNode, 'rest',
sample_to_surface_rh, 'source_file')
wflow.connect(sample_to_surface_rh, 'out_file',
outputNode, 'rh_surface_file')
return wflow
def init_autorecon_resume_wf(omp_nthreads, name='autorecon_resume_wf'):
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(fields=['subjects_dir', 'subject_id', 'use_T2']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['subjects_dir', 'subject_id', 'out_report']),
name='outputnode')
autorecon2_vol = pe.Node(fs.ReconAll(directive='autorecon2-volonly',
openmp=omp_nthreads),
name='autorecon2_vol')
autorecon2_vol.interface.num_threads = omp_nthreads
autorecon2_surfs = pe.MapNode(fs.ReconAll(directive='autorecon2-perhemi',
openmp=omp_nthreads),
iterfield='hemi',
name='autorecon2_surfs')
autorecon2_surfs.interface.num_threads = omp_nthreads
autorecon2_surfs.inputs.hemi = ['lh', 'rh']
autorecon_surfs = pe.MapNode(fs.ReconAll(directive='autorecon-hemi',
flags=[
'-noparcstats',
'-noparcstats2',
'-noparcstats3',
'-nohyporelabel',
'-nobalabels'
],
openmp=omp_nthreads),
iterfield='hemi',
name='autorecon_surfs')
autorecon_surfs.interface.num_threads = omp_nthreads
autorecon_surfs.inputs.hemi = ['lh', 'rh']
autorecon3 = pe.Node(ReconAllRPT(directive='autorecon3',
openmp=omp_nthreads,
generate_report=True),
name='autorecon3')
autorecon3.interface.num_threads = omp_nthreads
def _dedup(in_list):
vals = set(in_list)
if len(vals) > 1:
raise ValueError(
"Non-identical values can't be deduplicated:\n{!r}".format(
in_list))
return vals.pop()
workflow.connect([
(inputnode, autorecon_surfs, [('use_T2', 'use_T2')]),
(inputnode, autorecon2_vol, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(autorecon2_vol, autorecon2_surfs, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(autorecon2_surfs, autorecon_surfs,
[(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
(autorecon_surfs, autorecon3,
[(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
(autorecon3, outputnode, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id'),
('out_report', 'out_report')]),
])
return workflow
def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['t1w', 't2w', 'skullstripped_t1', 'subjects_dir']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=[
'subjects_dir', 'subject_id', 'fs_2_t1_transform', 'surfaces',
'out_report'
]),
name='outputnode')
def detect_inputs(t1w_list, t2w_list=[], hires_enabled=True):
from nipype.interfaces.base import isdefined
from nipype.utils.filemanip import filename_to_list
from nipype.interfaces.traits_extension import Undefined
import nibabel as nib
t1w_list = filename_to_list(t1w_list)
t2w_list = filename_to_list(t2w_list) if isdefined(t2w_list) else []
t1w_ref = nib.load(t1w_list[0])
# Use high resolution preprocessing if voxel size < 1.0mm
# Tolerance of 0.05mm requires that rounds down to 0.9mm or lower
hires = hires_enabled and max(t1w_ref.header.get_zooms()) < 1 - 0.05
t2w = Undefined
if t2w_list and max(nib.load(t2w_list[0]).header.get_zooms()) < 1.2:
t2w = t2w_list[0]
# https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon
mris_inflate = '-n 50' if hires else Undefined
return (t2w, isdefined(t2w), hires, mris_inflate)
recon_config = pe.Node(niu.Function(
function=detect_inputs,
output_names=['t2w', 'use_T2', 'hires', 'mris_inflate']),
name='recon_config',
run_without_submitting=True)
recon_config.inputs.hires_enabled = hires
def bidsinfo(in_file):
from fmriprep.interfaces.bids import BIDS_NAME
match = BIDS_NAME.search(in_file)
params = match.groupdict() if match is not None else {}
return tuple(
map(params.get, [
'subject_id', 'ses_id', 'task_id', 'acq_id', 'rec_id', 'run_id'
]))
bids_info = pe.Node(niu.Function(function=bidsinfo,
output_names=[
'subject_id', 'ses_id', 'task_id',
'acq_id', 'rec_id', 'run_id'
]),
name='bids_info',
run_without_submitting=True)
autorecon1 = pe.Node(fs.ReconAll(directive='autorecon1',
flags='-noskullstrip',
openmp=omp_nthreads),
name='autorecon1')
autorecon1.interface._can_resume = False
autorecon1.interface.num_threads = omp_nthreads
def inject_skullstripped(subjects_dir, subject_id, skullstripped):
import os
import nibabel as nib
from nilearn.image import resample_to_img, new_img_like
from nipype.utils.filemanip import copyfile
mridir = os.path.join(subjects_dir, subject_id, 'mri')
t1 = os.path.join(mridir, 'T1.mgz')
bm_auto = os.path.join(mridir, 'brainmask.auto.mgz')
bm = os.path.join(mridir, 'brainmask.mgz')
if not os.path.exists(bm_auto):
img = nib.load(t1)
mask = nib.load(skullstripped)
bmask = new_img_like(mask, mask.get_data() > 0)
resampled_mask = resample_to_img(bmask, img, 'nearest')
masked_image = new_img_like(
img,
img.get_data() * resampled_mask.get_data())
masked_image.to_filename(bm_auto)
if not os.path.exists(bm):
copyfile(bm_auto, bm, copy=True, use_hardlink=True)
return subjects_dir, subject_id
skull_strip_extern = pe.Node(niu.Function(
function=inject_skullstripped,
output_names=['subjects_dir', 'subject_id']),
name='skull_strip_extern')
fs_transform = pe.Node(fs.Tkregister2(fsl_out='freesurfer2subT1.mat',
reg_header=True),
name='fs_transform')
autorecon_resume_wf = init_autorecon_resume_wf(omp_nthreads=omp_nthreads)
gifti_surface_wf = init_gifti_surface_wf()
workflow.connect([
# Configuration
(inputnode, recon_config, [('t1w', 't1w_list'), ('t2w', 't2w_list')]),
(inputnode, bids_info, [(('t1w', fix_multi_T1w_source_name), 'in_file')
]),
# Passing subjects_dir / subject_id enforces serial order
(inputnode, autorecon1, [('subjects_dir', 'subjects_dir')]),
(bids_info, autorecon1, [('subject_id', 'subject_id')]),
(autorecon1, skull_strip_extern, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(skull_strip_extern, autorecon_resume_wf,
[('subjects_dir', 'inputnode.subjects_dir'),
('subject_id', 'inputnode.subject_id')]),
(autorecon_resume_wf, gifti_surface_wf,
[('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id')]),
# Reconstruction phases
(inputnode, autorecon1, [('t1w', 'T1_files')]),
(
recon_config,
autorecon1,
[
('t2w', 'T2_file'),
('hires', 'hires'),
# First run only (recon-all saves expert options)
('mris_inflate', 'mris_inflate')
]),
(inputnode, skull_strip_extern, [('skullstripped_t1', 'skullstripped')
]),
(recon_config, autorecon_resume_wf, [('use_T2', 'inputnode.use_T2')]),
# Construct transform from FreeSurfer conformed image to FMRIPREP
# reoriented image
(inputnode, fs_transform, [('t1w', 'target_image')]),
(autorecon1, fs_transform, [('T1', 'moving_image')]),
# Output
(autorecon_resume_wf, outputnode,
[('outputnode.subjects_dir', 'subjects_dir'),
('outputnode.subject_id', 'subject_id'),
('outputnode.out_report', 'out_report')]),
(gifti_surface_wf, outputnode, [('outputnode.surfaces', 'surfaces')]),
(fs_transform, outputnode, [('fsl_file', 'fs_2_t1_transform')]),
])
return workflow
def create_workflow(self, flow, inputnode, outputnode):
if self.config.seg_tool == "Freesurfer":
if self.config.use_existing_freesurfer_data is False:
# Converting to .mgz format
fs_mriconvert = pe.Node(interface=fs.MRIConvert(
out_type="mgz", out_file="T1.mgz"),
name="mgzConvert")
if self.config.make_isotropic:
fs_mriconvert.inputs.vox_size = (
self.config.isotropic_vox_size,
self.config.isotropic_vox_size,
self.config.isotropic_vox_size)
fs_mriconvert.inputs.resample_type = self.config.isotropic_interpolation
rename = pe.Node(util.Rename(), name='copyOrig')
orig_dir = os.path.join(self.config.freesurfer_subject_id,
"mri", "orig")
if not os.path.exists(orig_dir):
os.makedirs(orig_dir)
print("INFO : Folder not existing; %s created!" % orig_dir)
rename.inputs.format_string = os.path.join(orig_dir, "001.mgz")
if self.config.brain_mask_extraction_tool == "Freesurfer":
# ReconAll => named outputnode as we don't want to select a specific output....
fs_reconall = pe.Node(interface=fs.ReconAll(
flags='-no-isrunning -parallel -openmp {}'.format(
self.config.number_of_threads)),
name='reconall')
fs_reconall.inputs.directive = 'all'
fs_reconall.inputs.args = self.config.freesurfer_args
# fs_reconall.inputs.subjects_dir and fs_reconall.inputs.subject_id set in cmp/pipelines/diffusion/diffusion.py
fs_reconall.inputs.subjects_dir = self.config.freesurfer_subjects_dir
# fs_reconall.inputs.hippocampal_subfields_T1 = self.config.segment_hippocampal_subfields
# fs_reconall.inputs.brainstem = self.config.segment_brainstem
def isavailable(file):
# print "T1 is available"
return file
flow.connect([
(inputnode, fs_mriconvert, [(('T1', isavailable),
'in_file')]),
(fs_mriconvert, rename, [('out_file', 'in_file')]),
(rename, fs_reconall,
[(("out_file", extract_base_directory), "subject_id")
]),
(fs_reconall, outputnode,
[('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
])
else:
# ReconAll => named outputnode as we don't want to select a specific output....
fs_autorecon1 = pe.Node(interface=fs.ReconAll(
flags='-no-isrunning -parallel -openmp {}'.format(
self.config.number_of_threads)),
name='autorecon1')
fs_autorecon1.inputs.directive = 'autorecon1'
# if self.config.brain_mask_extraction_tool == "Custom" or self.config.brain_mask_extraction_tool == "ANTs":
if self.config.brain_mask_extraction_tool == "ANTs":
fs_autorecon1.inputs.flags = '-no-isrunning -noskullstrip -parallel -openmp {}'.format(
self.config.number_of_threads)
fs_autorecon1.inputs.args = self.config.freesurfer_args
# fs_reconall.inputs.subjects_dir and fs_reconall.inputs.subject_id set in cmp/pipelines/diffusion/diffusion.py
fs_autorecon1.inputs.subjects_dir = self.config.freesurfer_subjects_dir
def isavailable(file):
# print "Is available"
return file
flow.connect([(inputnode, fs_mriconvert, [
(('T1', isavailable), 'in_file')
]), (fs_mriconvert, rename, [('out_file', 'in_file')]),
(rename, fs_autorecon1,
[(("out_file", extract_base_directory),
"subject_id")])])
fs_source = pe.Node(interface=FreeSurferSource(),
name='fsSource')
fs_mriconvert_nu = pe.Node(interface=fs.MRIConvert(
out_type="niigz", out_file="nu.nii.gz"),
name='niigzConvert')
flow.connect([(fs_autorecon1, fs_source, [
('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')
]), (fs_source, fs_mriconvert_nu, [('nu', 'in_file')])])
fs_mriconvert_brainmask = pe.Node(
interface=fs.MRIConvert(out_type="mgz",
out_file="brainmask.mgz"),
name='fsMriconvertBETbrainmask')
if self.config.brain_mask_extraction_tool == "BET":
fsl_bet = pe.Node(interface=fsl.BET(
out_file='brain.nii.gz',
mask=True,
skull=True,
robust=True),
name='fsl_bet')
flow.connect([(fs_mriconvert_nu, fsl_bet,
[('out_file', 'in_file')]),
(fsl_bet, fs_mriconvert_brainmask,
[('out_file', 'in_file')])])
elif self.config.brain_mask_extraction_tool == "ANTs":
# templatefile =
# pkg_resources.resource_filename('cmtklib', os.path.join('data', 'segmentation',
# 'ants_template_IXI', 'T_template2_BrainCerebellum.nii.gz'))
# probmaskfile = pkg_resources.resource_filename('cmtklib',
# os.path.join('data', 'segmentation', 'ants_template_IXI',
# 'T_template_BrainCerebellumProbabilityMask.nii.gz'))
ants_bet = pe.Node(interface=ants.BrainExtraction(
out_prefix='ants_bet_'),
name='antsBET')
ants_bet.inputs.brain_template = self.config.ants_templatefile
ants_bet.inputs.brain_probability_mask = self.config.ants_probmaskfile
ants_bet.inputs.extraction_registration_mask = self.config.ants_regmaskfile
ants_bet.inputs.num_threads = self.config.number_of_threads
flow.connect([(fs_mriconvert_nu, ants_bet,
[('out_file', 'anatomical_image')]),
(ants_bet, fs_mriconvert_brainmask,
[('BrainExtractionBrain', 'in_file')])])
# elif self.config.brain_mask_extraction_tool == "Custom":
# fs_mriconvert_brainmask.inputs.in_file = os.path.abspath(
# self.config.brain_mask_path)
# copy_brainmask_to_fs = pe.Node(interface=copyFileToFreesurfer(),name='copy_brainmask_to_fs')
# copy_brainmask_to_fs.inputs.out_file =
# os.path.join(self.config.freesurfer_subject_id,"mri","brainmask.mgz")
# copy_brainmaskauto_to_fs = pe.Node(interface=copyFileToFreesurfer(),name='copy_brainmaskauto_to_fs')
# copy_brainmaskauto_to_fs.inputs.out_file =
# os.path.join(self.config.freesurfer_subject_id,"mri","brainmask.auto.mgz")
# flow.connect([
# (fs_mriconvert_brainmask,copy_brainmask_to_fs,[('out_file','in_file')]),
# (fs_mriconvert_brainmask,copy_brainmaskauto_to_fs,[('out_file','in_file')])
# ])
copy_brainmask_to_fs = pe.Node(
interface=copyBrainMaskToFreesurfer(),
name='copyBrainmaskTofs')
flow.connect([(rename, copy_brainmask_to_fs, [
(("out_file", extract_base_directory), "subject_dir")
]),
(fs_mriconvert_brainmask,
copy_brainmask_to_fs, [('out_file',
'in_file')])])
# flow.connect([
# (fs_source,fs_mriconvert_nu,[('nu','in_file')])
# ])
def get_freesurfer_subject_id(file):
# print("Extract reconall base dir : %s" % file[:-18])
return file[:-18]
fs_reconall23 = pe.Node(interface=fs.ReconAll(
flags='-no-isrunning -parallel -openmp {}'.format(
self.config.number_of_threads)),
name='reconall23')
fs_reconall23.inputs.directive = 'autorecon2'
fs_reconall23.inputs.args = self.config.freesurfer_args
fs_reconall23.inputs.flags = '-autorecon3'
# fs_reconall.inputs.subjects_dir and fs_reconall.inputs.subject_id set in cmp/pipelines/diffusion/diffusion.py
fs_reconall23.inputs.subjects_dir = self.config.freesurfer_subjects_dir
# fs_reconall.inputs.hippocampal_subfields_T1 = self.config.segment_hippocampal_subfields
# fs_reconall.inputs.brainstem = self.config.segment_brainstem
flow.connect([(copy_brainmask_to_fs, fs_reconall23, [
(("out_brainmask_file", get_freesurfer_subject_id),
"subject_id")
]),
(fs_reconall23, outputnode,
[('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')])])
else:
outputnode.inputs.subjects_dir = self.config.freesurfer_subjects_dir
outputnode.inputs.subject_id = self.config.freesurfer_subject_id
def init_autorecon_resume_wf(omp_nthreads, name='autorecon_resume_wf'):
r"""
Resume recon-all execution, assuming the `-autorecon1` stage has been completed.
In order to utilize resources efficiently, this is broken down into five
sub-stages; after the first stage, the second and third stages may be run
simultaneously, and the fourth and fifth stages may be run simultaneously,
if resources permit::
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon2-volonly
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon-hemi lh \
-noparcstats -nocortparc2 -noparcstats2 -nocortparc3 \
-noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg \
-noapas2aseg -nosegstats -nowmparc -nobalabels
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon-hemi rh \
-noparcstats -nocortparc2 -noparcstats2 -nocortparc3 \
-noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg \
-noapas2aseg -nosegstats -nowmparc -nobalabels
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon3 -hemi lh -T2pial
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-autorecon3 -hemi rh -T2pial
The excluded steps in the second and third stages (``-no<option>``) are not
fully hemisphere independent, and are therefore postponed to the final two
stages.
.. workflow::
:graph2use: orig
:simple_form: yes
from smriprep.workflows.surfaces import init_autorecon_resume_wf
wf = init_autorecon_resume_wf(omp_nthreads=1)
**Inputs**
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
use_T2
Refine pial surface using T2w image
use_FLAIR
Refine pial surface using FLAIR image
**Outputs**
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
"""
workflow = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['subjects_dir', 'subject_id', 'use_T2', 'use_FLAIR']),
name='inputnode')
outputnode = pe.Node(
niu.IdentityInterface(fields=['subjects_dir', 'subject_id']),
name='outputnode')
autorecon2_vol = pe.Node(fs.ReconAll(directive='autorecon2-volonly',
openmp=omp_nthreads),
n_procs=omp_nthreads,
mem_gb=5,
name='autorecon2_vol')
autorecon2_vol.interface._always_run = True
autorecon_surfs = pe.MapNode(fs.ReconAll(
directive='autorecon-hemi',
flags=[
'-noparcstats', '-nocortparc2', '-noparcstats2', '-nocortparc3',
'-noparcstats3', '-nopctsurfcon', '-nohyporelabel',
'-noaparc2aseg', '-noapas2aseg', '-nosegstats', '-nowmparc',
'-nobalabels'
],
openmp=omp_nthreads),
iterfield='hemi',
n_procs=omp_nthreads,
mem_gb=5,
name='autorecon_surfs')
autorecon_surfs.inputs.hemi = ['lh', 'rh']
autorecon_surfs.interface._always_run = True
autorecon3 = pe.MapNode(fs.ReconAll(directive='autorecon3',
openmp=omp_nthreads),
iterfield='hemi',
n_procs=omp_nthreads,
mem_gb=5,
name='autorecon3')
autorecon3.inputs.hemi = ['lh', 'rh']
autorecon3.interface._always_run = True
def _dedup(in_list):
vals = set(in_list)
if len(vals) > 1:
raise ValueError(
"Non-identical values can't be deduplicated:\n{!r}".format(
in_list))
return vals.pop()
workflow.connect([
(inputnode, autorecon3, [('use_T2', 'use_T2'),
('use_FLAIR', 'use_FLAIR')]),
(inputnode, autorecon2_vol, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(autorecon2_vol, autorecon_surfs, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(autorecon_surfs, autorecon3,
[(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
(autorecon3, outputnode, [(('subjects_dir', _dedup), 'subjects_dir'),
(('subject_id', _dedup), 'subject_id')]),
])
return workflow
def fs_Processing(data_dir, subject, tag):
'''
Parameters
----------
data_dir : str
path to the subject directory.
subject : str
subject id.
tag : str
containing the image type.
Returns
-------
all freesufer files at FS_Subjects_DIR
'''
datapath = data_dir+'/'+subject+'/anat' # raw image
datapathAlign = data_dir+'/'+subject+'/align'# rigid transformed
if os.path.exists(datapath) and os.listdir(datapath):
print('doing FS recon-all and hippocampal subfields...')
reconall = freesurfer.ReconAll()
reconall.inputs.subject_id = subject # Subject folder
reconall.inputs.directive = 'all'
FS_Subjects_DIR = "/usr/users/nmri/projects/tummala/FS_Subjects_DIR"
if not os.path.exists(FS_Subjects_DIR):
os.mkdir(FS_Subjects_DIR)
if tag == 'align':
if os.path.exists(datapathAlign) and os.listdir(datapathAlign):
print('doing recon-all on aligned images\n...')
FS_Subjects_Align = FS_Subjects_DIR+'/'+'FS_Subjects_Align'
if not os.path.exists(FS_Subjects_Align):
os.mkdir(FS_Subjects_Align)
reconall.inputs.subjects_dir = FS_Subjects_Align # Path to freesurfer subjects directory
alignimages = os.listdir(datapathAlign)
isT2, isFLAIR = doCheckforT2andFLAIR(datapathAlign)
for alignimage in alignimages:
if alignimage.endswith('reoriented.align.nii') and 'hrT1' in alignimage:
reconall.inputs.T1_files = datapathAlign+'/'+alignimage
elif alignimage.endswith('reoriented.align.nii') and (isT2 and not isFLAIR):
reconall.inputs.T2_file = datapathAlign+'/'+alignimage
reconall.inputs.use_T2 = True
elif alignimage.endswith('reoriented.align.nii') and isFLAIR:
reconall.inputs.FLAIR_file = datapathAlign+'/'+alignimage
reconall.inputs.use_FLAIR = True
else:
print(f'no align directory/no files in the align directory for {subject}\n')
elif tag == 'anat':
print('doing recon-all on anat images\n...')
FS_Subjects_Anat = FS_Subjects_DIR+'/'+'FS_Subjects_Anat'
if not os.path.exists(FS_Subjects_Anat):
os.mkdir(FS_Subjects_Anat)
reconall.inputs.subjects_dir = FS_Subjects_Anat # Path to freesurfer subjects directory
anatimages = os.listdir(datapath)
isT2, isFLAIR = doCheckforT2andFLAIR(datapath)
for anatimage in anatimages:
if anatimage.endswith('reoriented.nii') and 'hrT1' in anatimage:
reconall.inputs.T1_files = datapath+'/'+anatimage
elif anatimage.endswith('reoriented.nii') and (isT2 and not isFLAIR):
reconall.inputs.T2_file = datapath+'/'+anatimage
reconall.inputs.use_T2 = True
elif anatimage.endswith('reoriented.nii') and isFLAIR:
reconall.inputs.FLAIR_file = datapath+'/'+anatimage
reconall.inputs.use_FLAIR = True
reconall.inputs.hippocampal_subfields_T1 = True
reconall.run() # running the recon-all
else:
print(f'no anat directory/no files in anat directory for {subject}\n')
def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
r"""
Reconstruct anatomical surfaces using FreeSurfer's ``recon-all``.
Reconstruction is performed in three phases.
The first phase initializes the subject with T1w and T2w (if available)
structural images and performs basic reconstruction (``autorecon1``) with the
exception of skull-stripping.
For example, a subject with only one session with T1w and T2w images
would be processed by the following command::
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \
-i <bids-root>/sub-<subject_label>/anat/sub-<subject_label>_T1w.nii.gz \
-T2 <bids-root>/sub-<subject_label>/anat/sub-<subject_label>_T2w.nii.gz \
-autorecon1 \
-noskullstrip
The second phase imports an externally computed skull-stripping mask.
This workflow refines the external brainmask using the internal mask
implicit the the FreeSurfer's ``aseg.mgz`` segmentation,
to reconcile ANTs' and FreeSurfer's brain masks.
First, the ``aseg.mgz`` mask from FreeSurfer is refined in two
steps, using binary morphological operations:
1. With a binary closing operation the sulci are included
into the mask. This results in a smoother brain mask
that does not exclude deep, wide sulci.
2. Fill any holes (typically, there could be a hole next to
the pineal gland and the corpora quadrigemina if the great
cerebral brain is segmented out).
Second, the brain mask is grown, including pixels that have a high likelihood
to the GM tissue distribution:
3. Dilate and substract the brain mask, defining the region to search for candidate
pixels that likely belong to cortical GM.
4. Pixels found in the search region that are labeled as GM by ANTs
(during ``antsBrainExtraction.sh``) are directly added to the new mask.
5. Otherwise, estimate GM tissue parameters locally in patches of ``ww`` size,
and test the likelihood of the pixel to belong in the GM distribution.
This procedure is inspired on mindboggle's solution to the problem:
https://github.com/nipy/mindboggle/blob/7f91faaa7664d820fe12ccc52ebaf21d679795e2/mindboggle/guts/segment.py#L1660
The final phase resumes reconstruction, using the T2w image to assist
in finding the pial surface, if available.
See :py:func:`~smriprep.workflows.surfaces.init_autorecon_resume_wf` for details.
Memory annotations for FreeSurfer are based off `their documentation
<https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements>`_.
They specify an allocation of 4GB per subject. Here we define 5GB
to have a certain margin.
.. workflow::
:graph2use: orig
:simple_form: yes
from smriprep.workflows.surfaces import init_surface_recon_wf
wf = init_surface_recon_wf(omp_nthreads=1, hires=True)
**Parameters**
omp_nthreads : int
Maximum number of threads an individual process may use
hires : bool
Enable sub-millimeter preprocessing in FreeSurfer
**Inputs**
t1w
List of T1-weighted structural images
t2w
List of T2-weighted structural images (only first used)
flair
List of FLAIR images
skullstripped_t1
Skull-stripped T1-weighted image (or mask of image)
ants_segs
Brain tissue segmentation from ANTS ``antsBrainExtraction.sh``
corrected_t1
INU-corrected, merged T1-weighted image
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
**Outputs**
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
t1w2fsnative_xfm
LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space
fsnative2t1w_xfm
LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w
surfaces
GIFTI surfaces for gray/white matter boundary, pial surface,
midthickness (or graymid) surface, and inflated surfaces
out_brainmask
Refined brainmask, derived from FreeSurfer's ``aseg`` volume
out_aseg
FreeSurfer's aseg segmentation, in native T1w space
out_aparc
FreeSurfer's aparc+aseg segmentation, in native T1w space
**Subworkflows**
* :py:func:`~smriprep.workflows.surfaces.init_autorecon_resume_wf`
* :py:func:`~smriprep.workflows.surfaces.init_gifti_surface_wf`
"""
workflow = Workflow(name=name)
workflow.__desc__ = """\
Brain surfaces were reconstructed using `recon-all` [FreeSurfer {fs_ver},
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
""".format(fs_ver=fs.Info().looseversion() or '<ver>')
inputnode = pe.Node(niu.IdentityInterface(fields=[
't1w', 't2w', 'flair', 'skullstripped_t1', 'corrected_t1', 'ants_segs',
'subjects_dir', 'subject_id'
]),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=[
'subjects_dir', 'subject_id', 't1w2fsnative_xfm', 'fsnative2t1w_xfm',
'surfaces', 'out_brainmask', 'out_aseg', 'out_aparc'
]),
name='outputnode')
recon_config = pe.Node(FSDetectInputs(hires_enabled=hires),
name='recon_config')
fov_check = pe.Node(niu.Function(function=_check_cw256), name='fov_check')
autorecon1 = pe.Node(fs.ReconAll(directive='autorecon1',
openmp=omp_nthreads),
name='autorecon1',
n_procs=omp_nthreads,
mem_gb=5)
autorecon1.interface._can_resume = False
autorecon1.interface._always_run = True
skull_strip_extern = pe.Node(FSInjectBrainExtracted(),
name='skull_strip_extern')
fsnative2t1w_xfm = pe.Node(RobustRegister(auto_sens=True,
est_int_scale=True),
name='fsnative2t1w_xfm')
t1w2fsnative_xfm = pe.Node(LTAConvert(out_lta=True, invert=True),
name='t1w2fsnative_xfm')
autorecon_resume_wf = init_autorecon_resume_wf(omp_nthreads=omp_nthreads)
gifti_surface_wf = init_gifti_surface_wf()
aseg_to_native_wf = init_segs_to_native_wf()
aparc_to_native_wf = init_segs_to_native_wf(segmentation='aparc_aseg')
refine = pe.Node(RefineBrainMask(), name='refine')
workflow.connect([
# Configuration
(inputnode, recon_config, [('t1w', 't1w_list'), ('t2w', 't2w_list'),
('flair', 'flair_list')]),
# Passing subjects_dir / subject_id enforces serial order
(inputnode, autorecon1, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(autorecon1, skull_strip_extern, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(skull_strip_extern, autorecon_resume_wf,
[('subjects_dir', 'inputnode.subjects_dir'),
('subject_id', 'inputnode.subject_id')]),
(autorecon_resume_wf, gifti_surface_wf,
[('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id')]),
# Reconstruction phases
(inputnode, autorecon1, [('t1w', 'T1_files')]),
(inputnode, fov_check, [('t1w', 'in_files')]),
(fov_check, autorecon1, [('out', 'flags')]),
(
recon_config,
autorecon1,
[
('t2w', 'T2_file'),
('flair', 'FLAIR_file'),
('hires', 'hires'),
# First run only (recon-all saves expert options)
('mris_inflate', 'mris_inflate')
]),
(inputnode, skull_strip_extern, [('skullstripped_t1', 'in_brain')]),
(recon_config, autorecon_resume_wf, [('use_t2w', 'inputnode.use_T2'),
('use_flair',
'inputnode.use_FLAIR')]),
# Construct transform from FreeSurfer conformed image to sMRIPrep
# reoriented image
(inputnode, fsnative2t1w_xfm, [('t1w', 'target_file')]),
(autorecon1, fsnative2t1w_xfm, [('T1', 'source_file')]),
(fsnative2t1w_xfm, gifti_surface_wf, [('out_reg_file',
'inputnode.fsnative2t1w_xfm')]),
(fsnative2t1w_xfm, t1w2fsnative_xfm, [('out_reg_file', 'in_lta')]),
# Refine ANTs mask, deriving new mask from FS' aseg
(inputnode, refine, [('corrected_t1', 'in_anat'),
('ants_segs', 'in_ants')]),
(inputnode, aseg_to_native_wf, [('corrected_t1', 'inputnode.in_file')
]),
(autorecon_resume_wf, aseg_to_native_wf,
[('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id')]),
(inputnode, aparc_to_native_wf, [('corrected_t1', 'inputnode.in_file')
]),
(autorecon_resume_wf, aparc_to_native_wf,
[('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id')]),
(aseg_to_native_wf, refine, [('outputnode.out_file', 'in_aseg')]),
# Output
(autorecon_resume_wf, outputnode,
[('outputnode.subjects_dir', 'subjects_dir'),
('outputnode.subject_id', 'subject_id')]),
(gifti_surface_wf, outputnode, [('outputnode.surfaces', 'surfaces')]),
(t1w2fsnative_xfm, outputnode, [('out_lta', 't1w2fsnative_xfm')]),
(fsnative2t1w_xfm, outputnode, [('out_reg_file', 'fsnative2t1w_xfm')]),
(refine, outputnode, [('out_file', 'out_brainmask')]),
(aseg_to_native_wf, outputnode, [('outputnode.out_file', 'out_aseg')]),
(aparc_to_native_wf, outputnode, [('outputnode.out_file', 'out_aparc')
]),
])
return workflow
def freesurfer_preproc(wf, cfg, strat_pool, pipe_num, opt=None):
'''
{"name": "freesurfer_preproc",
"config": ["surface_analysis"],
"switch": ["run_freesurfer"],
"option_key": "None",
"option_val": "None",
"inputs": [["desc-preproc_T1w", "desc-reorient_T1w", "T1w"]],
"outputs": ["space-T1w_desc-brain_mask",
"freesurfer_subject_dir",
"label-CSF_mask",
"label-WM_mask",
"label-GM_mask",
"surface_curvature",
"pial_surface_mesh",
"smoothed_surface_mesh",
"spherical_surface_mesh",
"sulcal_depth_surface_maps",
"cortical_thickness_surface_maps",
"cortical_volume_surface_maps",
"white_matter_surface_mesh",
"raw_average"]}
'''
reconall = pe.Node(interface=freesurfer.ReconAll(),
name=f'anat_freesurfer_{pipe_num}')
freesurfer_subject_dir = os.path.join(
cfg.pipeline_setup['working_directory']['path'],
f'anat_preproc_freesurfer_{pipe_num}', 'anat_freesurfer')
if not os.path.exists(freesurfer_subject_dir):
os.makedirs(freesurfer_subject_dir)
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = freesurfer_subject_dir
reconall.inputs.openmp = cfg.pipeline_setup['system_config'][
'num_OMP_threads']
node, out = strat_pool.get_data(
["desc-preproc_T1w", "desc-reorient_T1w", "T1w"])
wf.connect(node, out, reconall, 'T1_files')
# register FS brain mask to native space
fs_brain_mask_to_native = pe.Node(interface=freesurfer.ApplyVolTransform(),
name='fs_brain_mask_to_native')
fs_brain_mask_to_native.inputs.reg_header = True
wf.connect(reconall, 'brainmask', fs_brain_mask_to_native, 'source_file')
wf.connect(reconall, 'rawavg', fs_brain_mask_to_native, 'target_file')
wf.connect(reconall, 'subjects_dir', fs_brain_mask_to_native,
'subjects_dir')
# convert brain mask file from .mgz to .nii.gz
fs_brain_mask_to_nifti = pe.Node(util.Function(input_names=['in_file'],
output_names=['out_file'],
function=mri_convert),
name='fs_brainmask_to_nifti')
wf.connect(fs_brain_mask_to_native, 'transformed_file',
fs_brain_mask_to_nifti, 'in_file')
# binarize the brain mask
binarize_fs_brain_mask = pe.Node(interface=fsl.maths.MathsCommand(),
name='binarize_fs_brainmask')
binarize_fs_brain_mask.inputs.args = '-bin'
wf.connect(fs_brain_mask_to_nifti, 'out_file', binarize_fs_brain_mask,
'in_file')
# fill holes
fill_fs_brain_mask = pe.Node(interface=afni.MaskTool(),
name='fill_fs_brainmask')
fill_fs_brain_mask.inputs.fill_holes = True
fill_fs_brain_mask.inputs.outputtype = 'NIFTI_GZ'
wf.connect(binarize_fs_brain_mask, 'out_file', fill_fs_brain_mask,
'in_file')
# register FS segmentations (aseg.mgz) to native space
fs_aseg_to_native = pe.Node(interface=freesurfer.ApplyVolTransform(),
name='fs_aseg_to_native')
fs_aseg_to_native.inputs.reg_header = True
fs_aseg_to_native.inputs.interp = 'nearest'
fs_aseg_to_native.inputs.subjects_dir = freesurfer_subject_dir
wf.connect(reconall, 'aseg', fs_aseg_to_native, 'source_file')
wf.connect(reconall, 'rawavg', fs_aseg_to_native, 'target_file')
# convert registered FS segmentations from .mgz to .nii.gz
fs_aseg_to_nifti = pe.Node(util.Function(input_names=['in_file'],
output_names=['out_file'],
function=mri_convert),
name='fs_aseg_to_nifti')
fs_aseg_to_nifti.inputs.args = '-rt nearest'
wf.connect(fs_aseg_to_native, 'transformed_file', fs_aseg_to_nifti,
'in_file')
pick_tissue = pe.Node(util.Function(
input_names=['multiatlas_Labels'],
output_names=['csf_mask', 'gm_mask', 'wm_mask'],
function=pick_tissue_from_labels_file),
name=f'anat_preproc_freesurfer_tissue_mask')
pick_tissue.inputs.include_ventricles = True
wf.connect(fs_aseg_to_nifti, 'out_file', pick_tissue, 'multiatlas_Labels')
outputs = {
'space-T1w_desc-brain_mask': (fill_fs_brain_mask, 'out_file'),
'freesurfer_subject_dir': (reconall, 'subjects_dir'),
'label-CSF_mask': (pick_tissue, 'csf_mask'),
'label-WM_mask': (pick_tissue, 'wm_mask'),
'label-GM_mask': (pick_tissue, 'gm_mask'),
'surface_curvature': (reconall, 'curv'),
'pial_surface_mesh': (reconall, 'pial'),
'smoothed_surface_mesh': (reconall, 'smoothwm'),
'spherical_surface_mesh': (reconall, 'sphere'),
'sulcal_depth_surface_maps': (reconall, 'sulc'),
'cortical_thickness_surface_maps': (reconall, 'thickness'),
'cortical_volume_surface_maps': (reconall, 'volume'),
'white_matter_surface_mesh': (reconall, 'white'),
'raw_average': (reconall, 'rawavg')
}
return (wf, outputs)