def check_input1(self, gui=True):
print '**** Check Inputs ****'
diffusion_available = False
bvecs_available = False
bvals_available = False
t1_available = False
t2_available = False
valid_inputs = False
dwi_file = os.path.join(self.subject_directory, 'dwi',
self.subject + '_dwi.nii.gz')
bval_file = os.path.join(self.subject_directory, 'dwi',
self.subject + '_dwi.bval')
bvec_file = os.path.join(self.subject_directory, 'dwi',
self.subject + '_dwi.bvec')
T1_file = os.path.join(self.subject_directory, 'anat',
self.subject + '_T1w.nii.gz')
T2_file = os.path.join(self.subject_directory, 'anat',
self.subject + '_T2w.nii.gz')
print "Looking for...."
print "dwi_file : %s" % dwi_file
print "bvecs_file : %s" % bvec_file
print "bvals_file : %s" % bval_file
print "T1_file : %s" % T1_file
print "T2_file : %s" % T2_file
try:
layout = BIDSLayout(self.base_directory)
print "Valid BIDS dataset with %s subjects" % len(
layout.get_subjects())
for subj in layout.get_subjects():
self.global_conf.subjects.append('sub-' + str(subj))
# self.global_conf.subjects = ['sub-'+str(subj) for subj in layout.get_subjects()]
self.global_conf.modalities = [
str(mod) for mod in layout.get_modalities()
]
# mods = layout.get_modalities()
types = layout.get_types()
# print "Available modalities :"
# for mod in mods:
# print "-%s" % mod
for typ in types:
if typ == 'dwi' and os.path.isfile(dwi_file):
print "%s available" % typ
diffusion_available = True
if typ == 'T1w' and os.path.isfile(T1_file):
print "%s available" % typ
t1_available = True
if typ == 'T2w' and os.path.isfile(T2_file):
print "%s available" % typ
t2_available = True
except:
error(
message=
"Invalid BIDS dataset. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
if os.path.isfile(bval_file): bvals_available = True
if os.path.isfile(bvec_file): bvecs_available = True
mem = Memory(base_dir=os.path.join(self.derivatives_directory, 'cmp',
self.subject, 'tmp', 'nipype'))
swap_and_reorient = mem.cache(SwapAndReorient)
if diffusion_available:
if bvals_available and bvecs_available:
self.stages[
'Diffusion'].config.diffusion_imaging_model_choices = self.diffusion_imaging_model
#Copy diffusion data to derivatives / cmp / subject / dwi
out_dwi_file = os.path.join(self.derivatives_directory, 'cmp',
self.subject, 'dwi',
self.subject + '_dwi.nii.gz')
out_bval_file = os.path.join(self.derivatives_directory, 'cmp',
self.subject, 'dwi',
self.subject + '_dwi.bval')
out_bvec_file = os.path.join(self.derivatives_directory, 'cmp',
self.subject, 'dwi',
self.subject + '_dwi.bvec')
shutil.copy(src=dwi_file, dst=out_dwi_file)
shutil.copy(src=bvec_file, dst=out_bvec_file)
shutil.copy(src=bval_file, dst=out_bval_file)
if t2_available:
print "Swap and reorient T2"
swap_and_reorient(
src_file=os.path.join(self.subject_directory, 'anat',
self.subject + '_T2w.nii.gz'),
ref_file=os.path.join(self.subject_directory, 'dwi',
self.subject + '_dwi.nii.gz'),
out_file=os.path.join(self.derivatives_directory,
'cmp', self.subject, 'anat',
self.subject + '_T2w.nii.gz'))
if t1_available:
swap_and_reorient(
src_file=os.path.join(self.subject_directory, 'anat',
self.subject + '_T1w.nii.gz'),
ref_file=os.path.join(self.subject_directory, 'dwi',
self.subject + '_dwi.nii.gz'),
out_file=os.path.join(self.derivatives_directory,
'cmp', self.subject, 'anat',
self.subject + '_T1w.nii.gz'))
valid_inputs = True
input_message = 'Inputs check finished successfully.\nDiffusion and morphological data available.'
else:
input_message = 'Error during inputs check.\nMorphological data (T1) not available.'
else:
input_message = 'Error during inputs check.\nDiffusion bvec or bval files not available.'
elif t1_available:
input_message = 'Error during inputs check. \nDiffusion data not available (DSI/DTI/HARDI).'
else:
input_message = 'Error during inputs check. No diffusion or morphological data available in folder ' + os.path.join(
self.base_directory, 'RAWDATA') + '!'
#diffusion_imaging_model = diffusion_imaging_model[0]
if gui:
#input_notification = Check_Input_Notification(message=input_message, diffusion_imaging_model_options=diffusion_imaging_model,diffusion_imaging_model=diffusion_imaging_model)
#input_notification.configure_traits()
print input_message
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
# diffusion_file = os.path.join(self.subject_directory,'dwi',self.subject+'_dwi.nii.gz')
# n_vol = nib.load(diffusion_file).shape[3]
# if self.stages['Preprocessing'].config.end_vol == 0 or self.stages['Preprocessing'].config.end_vol == self.stages['Preprocessing'].config.max_vol or self.stages['Preprocessing'].config.end_vol >= n_vol-1:
# self.stages['Preprocessing'].config.end_vol = n_vol-1
# self.stages['Preprocessing'].config.max_vol = n_vol-1
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
else:
print input_message
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
# diffusion_file = os.path.join(self.subject_directory,'dwi',self.subject+'_dwi.nii.gz')
# n_vol = nib.load(diffusion_file).shape[3]
# if self.stages['Preprocessing'].config.end_vol == 0 or self.stages['Preprocessing'].config.end_vol == self.stages['Preprocessing'].config.max_vol or self.stages['Preprocessing'].config.end_vol >= n_vol-1:
# self.stages['Preprocessing'].config.end_vol = n_vol-1
# self.stages['Preprocessing'].config.max_vol = n_vol-1
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
if t2_available:
self.stages['Registration'].config.registration_mode_trait = [
'Linear + Non-linear (FSL)'
] #,'BBregister (FS)','Nonlinear (FSL)']
if (t1_available and diffusion_available):
valid_inputs = True
else:
print "Missing required inputs."
error(
message=
"Missing required inputs. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
for stage in self.stages.values():
if stage.enabled:
print stage.name
print stage.stage_dir
self.fill_stages_outputs()
return valid_inputs
def check_input(self, layout, gui=True):
print '**** Check Inputs ****'
diffusion_available = False
bvecs_available = False
bvals_available = False
valid_inputs = False
if self.global_conf.subject_session == '':
subject = self.subject
else:
subject = "_".join(
(self.subject, self.global_conf.subject_session))
dwi_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.nii.gz')
bval_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.bval')
bvec_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.bvec')
subjid = self.subject.split("-")[1]
try:
layout = BIDSLayout(self.base_directory)
print "Valid BIDS dataset with %s subjects" % len(
layout.get_subjects())
for subj in layout.get_subjects():
self.global_conf.subjects.append('sub-' + str(subj))
# self.global_conf.subjects = ['sub-'+str(subj) for subj in layout.get_subjects()]
self.global_conf.modalities = [
str(mod) for mod in layout.get_modalities()
]
# mods = layout.get_modalities()
types = layout.get_types()
# print "Available modalities :"
# for mod in mods:
# print "-%s" % mod
if self.global_conf.subject_session == '':
files = layout.get(subject=subjid,
type='dwi',
extensions='.nii.gz')
if len(files) > 0:
dwi_file = files[0].filename
print dwi_file
else:
error(message="Diffusion image not found for subject %s." %
(subjid),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
type='dwi',
extensions='.bval')
if len(files) > 0:
bval_file = files[0].filename
print bval_file
else:
error(
message="Diffusion bval image not found for subject %s."
% (subjid),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
type='dwi',
extensions='.bvec')
if len(files) > 0:
bvec_file = files[0].filename
print bvec_file
else:
error(
message="Diffusion bvec image not found for subject %s."
% (subjid),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
else:
sessid = self.global_conf.subject_session.split("-")[1]
files = layout.get(subject=subjid,
type='dwi',
extensions='.nii.gz',
session=sessid)
if len(files) > 0:
dwi_file = files[0].filename
print dwi_file
else:
error(
message=
"Diffusion image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
type='dwi',
extensions='.bval',
session=sessid)
if len(files) > 0:
bval_file = files[0].filename
print bval_file
else:
error(
message=
"Diffusion bval image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
type='dwi',
extensions='.bvec',
session=sessid)
if len(files) > 0:
bvec_file = files[0].filename
print bvec_file
else:
error(
message=
"Diffusion bvec image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
print "Looking for...."
print "dwi_file : %s" % dwi_file
print "bvecs_file : %s" % bvec_file
print "bvals_file : %s" % bval_file
for typ in types:
if typ == 'dwi' and os.path.isfile(dwi_file):
print "%s available" % typ
diffusion_available = True
except:
error(
message=
"Invalid BIDS dataset. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
if os.path.isfile(bval_file): bvals_available = True
if os.path.isfile(bvec_file): bvecs_available = True
if diffusion_available:
if bvals_available and bvecs_available:
self.stages[
'Diffusion'].config.diffusion_imaging_model_choices = self.diffusion_imaging_model
#Copy diffusion data to derivatives / cmp / subject / dwi
if self.global_conf.subject_session == '':
out_dwi_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.nii.gz')
out_bval_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.bval')
out_bvec_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.bvec')
else:
out_dwi_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.nii.gz')
out_bval_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.bval')
out_bvec_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.bvec')
if not os.path.isfile(out_dwi_file):
shutil.copy(src=dwi_file, dst=out_dwi_file)
if not os.path.isfile(out_bvec_file):
shutil.copy(src=bvec_file, dst=out_bvec_file)
if not os.path.isfile(out_bval_file):
shutil.copy(src=bval_file, dst=out_bval_file)
valid_inputs = True
input_message = 'Inputs check finished successfully.\nDiffusion and morphological data available.'
else:
input_message = 'Error during inputs check.\nDiffusion bvec or bval files not available.'
else:
if self.global_conf.subject_session == '':
input_message = 'Error during inputs check. No diffusion data available in folder ' + os.path.join(
self.base_directory, self.subject, 'dwi') + '!'
else:
input_message = 'Error during inputs check. No diffusion data available in folder ' + os.path.join(
self.base_directory, self.subject,
self.global_conf.subject_session, 'dwi') + '!'
#diffusion_imaging_model = diffusion_imaging_model[0]
if gui:
#input_notification = Check_Input_Notification(message=input_message, diffusion_imaging_model_options=diffusion_imaging_model,diffusion_imaging_model=diffusion_imaging_model)
#input_notification.configure_traits()
print input_message
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
# if diffusion_available:
# n_vol = nib.load(dwi_file).shape[3]
# if self.stages['Preprocessing'].config.end_vol == 0 or self.stages['Preprocessing'].config.end_vol == self.stages['Preprocessing'].config.max_vol or self.stages['Preprocessing'].config.end_vol >= n_vol-1:
# self.stages['Preprocessing'].config.end_vol = n_vol-1
# self.stages['Preprocessing'].config.max_vol = n_vol-1
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
else:
print input_message
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
# if diffusion_available:
# n_vol = nib.load(dwi_file).shape[3]
# if self.stages['Preprocessing'].config.end_vol == 0 or self.stages['Preprocessing'].config.end_vol == self.stages['Preprocessing'].config.max_vol or self.stages['Preprocessing'].config.end_vol >= n_vol-1:
# self.stages['Preprocessing'].config.end_vol = n_vol-1
# self.stages['Preprocessing'].config.max_vol = n_vol-1
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
if (diffusion_available):
valid_inputs = True
else:
print "Missing required inputs."
error(
message=
"Missing diffusion inputs. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
for stage in self.stages.values():
if stage.enabled:
print stage.name
print stage.stage_dir
self.fill_stages_outputs()
return valid_inputs
def bidsPipeline(resultsDir, workDir, subDir, subid):
layout = BIDSLayout("/ds102/")
subjects = layout.get_subjects()
mods = layout.get_modalities()
mod_types = layout.get_types(modality='func')
tasks = layout.get_tasks()
