def configure_spm(matlab_exec=None, spm_dir=None):
origin_spm_dir = spm_dir
# configure SPM
if "SPM_DIR" in os.environ:
spm_dir = os.environ["SPM_DIR"]
if not spm_dir is None:
spm_dir = _expand_path(spm_dir)
if spm_dir is None or not os.path.isdir(spm_dir):
if spm_dir:
print "Path %s doesn't exist" % spm_dir
print "spm_dir defaulting to %s" % DEFAULT_SPM_DIR
spm_dir = DEFAULT_SPM_DIR
assert os.path.exists(spm_dir), (
"Can't find SPM path '%s'! You should export SPM_DIR=/path/to/" "your/SPM/root/dir" % spm_dir
)
if (
distutils.version.LooseVersion(nipype.__version__).version >= [0, 9]
and os.path.exists("/i2bm/local/bin/spm8")
and origin_spm_dir is None
):
if "SPM8_MCR" in os.environ:
matlab_cmd = "%s run script" % os.environ["SPM8_MCR"]
else:
matlab_cmd = "/i2bm/local/bin/spm8 run script"
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
else:
matlab.MatlabCommand.set_default_paths(spm_dir)
# configure MATLAB
if "MATLAB_EXEC" in os.environ:
matlab_exec = os.environ["MATLAB_EXEC"]
if not matlab_exec is None:
matlab_exec = _expand_path(matlab_exec)
if matlab_exec is None or not os.path.exists(matlab_exec):
if matlab_exec:
print "Path %s doesn't exist" % matlab_exec
matlab_exec = DEFAULT_MATLAB_EXEC
if not os.path.exists(matlab_exec):
m_choices = glob.glob("/neurospin/local/matlab/R*/bin/matlab")
if m_choices:
matlab_exec = m_choices[0]
assert os.path.exists(matlab_exec), (
"Can't find matlab path: '%s' ! You should export MATLAB_EXEC="
"/path/to/your/matlab/exec, doesn't exist; you need to export "
"matlab_exec" % matlab_exec
)
matlab.MatlabCommand.set_default_matlab_cmd(matlab_exec)
return spm_dir, matlab_exec
def configure_spm(matlab_exec=None, spm_dir=None):
# configure MATLAB
if 'MATLAB_EXEC' in os.environ:
matlab_exec = os.environ['MATLAB_EXEC']
# use SPM_MCR defined by environment variable
if (distutils.version.LooseVersion(nipype.__version__).version >= [0, 9]
and 'SPM_MCR' in os.environ
and os.path.exists(os.environ['SPM_MCR'])):
spm_dir = os.environ['SPM_DIR']
matlab_cmd = '%s run script' % os.environ['SPM_MCR']
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
# use hard coded SPM_MCR
elif (distutils.version.LooseVersion(nipype.__version__).version >= [0, 9]
and os.path.exists('/i2bm/local/bin/spm8')):
spm_dir = '/i2bm/local/spm8-standalone/spm8_mcr/spm8'
matlab_cmd = '/i2bm/local/bin/spm8 run script'
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
# use Matlab with SPM toolbox
else:
# try real hard to find matlab only if not using the mcr
if not matlab_exec is None:
matlab_exec = _expand_path(matlab_exec)
if matlab_exec is None or not os.path.exists(matlab_exec):
if matlab_exec:
print "Path %s doesn't exist" % matlab_exec
matlab_exec = DEFAULT_MATLAB_EXEC
if not os.path.exists(matlab_exec):
m_choices = glob.glob("/neurospin/local/matlab/R*/bin/matlab")
if m_choices:
matlab_exec = m_choices[0]
assert os.path.exists(matlab_exec), (
"Can't find matlab path: '%s' ! You should export MATLAB_EXEC="
"/path/to/your/matlab/exec, doesn't exist; you need to export "
"matlab_exec" % matlab_exec)
matlab.MatlabCommand.set_default_matlab_cmd(matlab_exec)
# configure SPM
if 'SPM_DIR' in os.environ and spm_dir is None:
spm_dir = os.environ['SPM_DIR']
if not spm_dir is None:
spm_dir = _expand_path(spm_dir)
if spm_dir is None or not os.path.isdir(spm_dir):
if spm_dir:
print "Path %s doesn't exist" % spm_dir
print "spm_dir defaulting to %s" % DEFAULT_SPM_DIR
spm_dir = DEFAULT_SPM_DIR
assert os.path.exists(spm_dir), (
"Can't find SPM path '%s'! You should export SPM_DIR=/path/to/"
"your/SPM/root/dir" % spm_dir)
matlab.MatlabCommand.set_default_paths(spm_dir)
return spm_dir, matlab_exec
def _generate_preproc_pipeline(jobfile, dataset_dir=None,
options_callback=None, **kwargs):
"""
Generate pipeline (i.e subject factor + preproc params) from
config file.
Returns
-------
subjects: list of `SubjectData` objects
subject list
preproc_params: dict
preproc parameters
"""
# read config file
jobfile = os.path.abspath(jobfile)
options = _parse_job(jobfile, **kwargs)
options = _del_nones_from_dict(options)
# generate subject conf
if dataset_dir is None:
assert "dataset_dir" in options, (
"dataset_dir not specified (neither in jobfile"
" nor in this function call)")
dataset_dir = options["dataset_dir"]
else:
assert not dataset_dir is None, (
"dataset_dir not specified (neither in jobfile"
" nor in this function call")
assert dataset_dir
options["dataset_dir"] = dataset_dir
if not isinstance(dataset_dir, basestring):
tmp = [_generate_preproc_pipeline(
jobfile, dataset_dir=dsd,
options_callback=options_callback, **kwargs)
for dsd in dataset_dir]
subjects = [subject for x in tmp for subject in x[0]]
return subjects, tmp[0][1]
if options_callback:
options = options_callback(options)
dataset_dir = options["dataset_dir"]
dataset_dir = _expand_path(dataset_dir)
assert os.path.isdir(dataset_dir), (
"dataset_dir %s doesn't exist" % dataset_dir)
# output dir
output_dir = _expand_path(options["output_dir"],
relative_to=dataset_dir)
if output_dir is None:
raise RuntimeError(
("Could not expand 'output_dir' specified in %s: invalid"
" path %s (relative to directory %s)") % (
jobfile, options["output_dir"], dataset_dir))
# dataset description
dataset_description = options.get("dataset_description", None)
# how many subjects ?
subjects = []
nsubjects = options.get('nsubjects', np.inf)
exclude_these_subject_ids = options.get(
'exclude_these_subject_ids', [])
include_only_these_subject_ids = options.get(
'include_only_these_subject_ids', [])
def _ignore_subject(subject_id):
"""
Ignore given subject_id ?
"""
if subject_id in exclude_these_subject_ids:
return True
elif len(include_only_these_subject_ids
) and not subject_id in include_only_these_subject_ids:
return True
else:
return False
# subject data factory
subject_dir_wildcard = os.path.join(dataset_dir,
options.get("subject_dirs",
"*"))
sessions = [k for k in options.keys() if re.match("session_.+_func", k)]
session_ids = [re.match("session_(.+)_func", session).group(1)
for session in sessions]
assert len(sessions) > 0
subject_data_dirs = sorted(glob.glob(subject_dir_wildcard))
assert subject_data_dirs, (
"No subject directories found for wildcard: %s" % (
subject_dir_wildcard))
for subject_data_dir in subject_data_dirs:
if len(subjects) == nsubjects:
break
subject_id = os.path.basename(subject_data_dir)
if _ignore_subject(subject_id):
continue
subject_output_dir = os.path.join(output_dir, subject_id)
# grab functional data
func = []
sess_output_dirs = []
skip_subject = False
for session in sessions:
session = options[session]
sess_func_wildcard = os.path.join(subject_data_dir, session)
sess_func = sorted(glob.glob(sess_func_wildcard))
if not sess_func:
print("subject %s: No func images found for"
" wildcard %s" % (subject_id, sess_func_wildcard))
skip_subject = True
break
sess_dir = os.path.dirname(sess_func[0])
if len(sess_func) == 1:
sess_func = sess_func[0]
func.append(sess_func)
# session output dir
if os.path.basename(sess_dir) != os.path.basename(
subject_output_dir):
sess_output_dir = os.path.join(
subject_output_dir, get_relative_path(subject_data_dir,
sess_dir))
else:
sess_output_dir = subject_output_dir
if not os.path.exists(sess_output_dir):
os.makedirs(sess_output_dir)
sess_output_dirs.append(sess_output_dir)
if skip_subject:
print "Skipping subject %s" % subject_id
continue
# grab anat
anat = None
if not options.get("anat", None) is None:
anat_wildcard = os.path.join(subject_data_dir, options['anat'])
anat = glob.glob(anat_wildcard)
# skip subject if anat absent
if len(anat) < 1:
print (
"subject %s: anat image matching %s not found!; skipping"
" subject" % (subject_id, anat_wildcard))
continue
anat = anat[0]
anat_dir = os.path.dirname(anat)
else:
anat = None
anat_dir = ""
# anat output dir
anat_output_dir = None
if anat_dir:
anat_output_dir = os.path.join(subject_output_dir,
get_relative_path(subject_data_dir,
anat_dir))
if not os.path.exists(anat_output_dir):
os.makedirs(anat_output_dir)
# make subject data
subject_data = SubjectData(subject_id=subject_id, func=func, anat=anat,
output_dir=subject_output_dir,
session_output_dirs=sess_output_dirs,
anat_output_dir=anat_output_dir,
session_id=session_ids,
data_dir=subject_data_dir)
subjects.append(subject_data)
print "No subjects globbed (dataset_dir=%s, subject_dir_wildcard=%s" % (
dataset_dir, subject_dir_wildcard)
# preproc parameters
preproc_params = {
"spm_dir": options.get("spm_dir", None),
"matlab_exec": options.get("matlab_exec", None),
"report": options.get("report", True),
"output_dir": output_dir,
"dataset_id": options.get("dataset_id", dataset_dir),
"n_jobs": options.get("n_jobs", None),
"caching": options.get("caching", True),
"cv_tc": options.get("cv_tc", True),
"dataset_description": dataset_description,
"slice_timing_software": options.get("slice_timing_software", "spm"),
"realign_software": options.get("realign_software", "spm"),
"coregister_software": options.get("coregister_software", "spm"),
}
# delete orientation meta-data ?
preproc_params['deleteorient'] = options.get(
"deleteorient", False)
# configure slice-timing correction node
preproc_params["slice_timing"] = not options.get(
"disable_slice_timing", False)
# can't do STC without TR
if preproc_params["slice_timing"]:
preproc_params.update(dict((k, options.get(k, None))
for k in ["TR", "TA", "slice_order",
"interleaved"]))
if preproc_params["TR"] is None:
preproc_params["slice_timing"] = False
# configure motion correction node
preproc_params["realign"] = not options.get("disable_realign", False)
if preproc_params["realign"]:
preproc_params['realign_reslice'] = options.get("reslice_realign",
False)
preproc_params['register_to_mean'] = options.get("register_to_mean",
True)
# configure coregistration node
preproc_params["coregister"] = not options.get("disable_coregister",
False)
if preproc_params["coregister"]:
preproc_params['coregister_reslice'] = options["coregister_reslice"]
preproc_params['coreg_anat_to_func'] = not options.get(
"coreg_func_to_anat", True)
# configure tissue segmentation node
preproc_params["segment"] = not options.get("disable_segment", False)
if preproc_params["segment"]:
pass # XXX pending code...
# configure normalization node
preproc_params["normalize"] = not options.get(
"disable_normalize", False)
preproc_params['func_write_voxel_sizes'] = options.get(
"func_voxel_sizes", [3, 3, 3])
preproc_params['anat_write_voxel_sizes'] = options.get(
"anat_voxel_sizes", [1, 1, 1])
preproc_params['dartel'] = options.get("dartel", False)
# configure smoothing node
preproc_params["fwhm"] = options.get("fwhm", 0.)
return subjects, preproc_params
def _generate_preproc_pipeline(config_file,
dataset_dir=None,
output_dir=None,
scratch=None,
options_callback=None,
**kwargs):
"""
Generate pipeline (i.e subject factor + preproc params) from
config file.
dataset_dir, and output_dir can be specified in config_file, passed as
function argument, or exported in environ variables like so:
OUTPUT_DIR=/some/dir, etc.
Returns
-------
subjects: list of `SubjectData` objects
subject list
preproc_params: dict
preproc parameters
"""
# read config file
config_file = os.path.abspath(config_file)
options = _parse_job(config_file, **kwargs)
options = _del_nones_from_dict(options)
# sanitize output_dir and dataset_dir
dataset_dir = os.environ.get("DATASET_DIR", dataset_dir)
output_dir = os.environ.get("OUTPUT_DIR", output_dir)
scratch = os.environ.get("SCRATCH", scratch)
for item in ["dataset_dir", "output_dir", "scratch"]:
val = eval(item)
if val is None:
if item not in options:
# get value from environ (if exists)
val = os.environ.get(item.upper(), val)
if val is None and item in ["dataset_dir", "output_dir"]:
raise ValueError(
("%s not specified (neither in environ variable, "
"nor in config_file nor in this function "
"call)") % item)
# set value from environ
if item == "dataset_dir":
dataset_dir = val
elif item == "output_dir":
output_dir = val
options["dataset_dir"] = dataset_dir = (
dataset_dir if dataset_dir is not None else options["dataset_dir"])
options["output_dir"] = output_dir = (output_dir if output_dir is not None
else options["output_dir"])
options["scratch"] = scratch = (scratch if scratch is not None else
options.get("scratch", output_dir))
assert options["dataset_dir"]
assert options["output_dir"]
# load data from multiple dataset_dirs
if not isinstance(dataset_dir, basestring):
kwargs["output_dir"] = output_dir
tmp = [
_generate_preproc_pipeline(config_file,
dataset_dir=dsd,
options_callback=options_callback,
**kwargs) for dsd in dataset_dir
]
subjects = [subject for x in tmp for subject in x[0]]
return subjects, tmp[0][1]
# invoke callback
if options_callback:
options = options_callback(options)
if dataset_dir is None:
dataset_dir = options.get("dataset_dir", None)
if output_dir is None:
output_dir = options.get("output_dir", None)
if scratch is None:
output_dir = options.get("scratch", None)
# check dataset_dir
dataset_dir = _expand_path(dataset_dir)
if not os.path.isdir(dataset_dir):
raise OSError("dataset_dir '%s' doesn't exist" % dataset_dir)
# check output_dir
output_dir = _expand_path(options["output_dir"], relative_to=dataset_dir)
scratch = _expand_path(options["scratch"], relative_to=dataset_dir)
if output_dir is None:
raise OSError(("Could not expand 'output_dir' specified in %s: invalid"
" path %s (relative to directory %s)") %
(config_file, options["output_dir"], dataset_dir))
# dataset description
dataset_description = options.get("dataset_description", None)
# preproc parameters
preproc_params = {
"spm_dir": options.get("spm_dir", None),
"matlab_exec": options.get("matlab_exec", None),
"report": options.get("report", True),
"output_dir": output_dir,
"scratch": scratch,
"dataset_id": options.get("dataset_id", dataset_dir),
"n_jobs": options.get("n_jobs", None),
"caching": options.get("caching", True),
"tsdiffana": options.get("tsdiffana", True),
"dataset_description": dataset_description,
"slice_timing_software": options.get("slice_timing_software", "spm"),
"realign_software": options.get("realign_software", "spm"),
"coregister_software": options.get("coregister_software", "spm"),
"smooth_software": options.get("smooth_software", "spm")
}
# delete orientation meta-data ?
preproc_params['deleteorient'] = options.get("deleteorient", False)
# configure slice-timing correction node
preproc_params["slice_timing"] = not options.get("disable_slice_timing",
False)
# can't do STC without TR
if preproc_params["slice_timing"]:
preproc_params.update(
dict((k, options.get(k, None))
for k in ["TR", "TA", "slice_order", "interleaved"]))
if preproc_params["TR"] is None:
preproc_params["slice_timing"] = False
# configure motion correction node
preproc_params["realign"] = not options.get("disable_realign", False)
if preproc_params["realign"]:
preproc_params['realign_reslice'] = options.get(
"reslice_realign", False)
preproc_params['register_to_mean'] = options.get(
"register_to_mean", True)
# configure coregistration node
preproc_params["coregister"] = not options.get("disable_coregister", False)
if preproc_params["coregister"]:
preproc_params['coregister_reslice'] = options.get(
"coregister_reslice")
preproc_params['coreg_anat_to_func'] = not options.get(
"coreg_func_to_anat", True)
# configure tissue segmentation node
preproc_params["segment"] = not options.get("disable_segment", False)
preproc_params["newsegment"] = options.get(
"newsegment", False) and preproc_params["segment"]
# configure normalization node
preproc_params["normalize"] = not options.get("disable_normalize", False)
# configure output voxel sizes
for brain in ["func", "anat"]:
k = "%s_write_voxel_size" % brain
ks = k + "s"
if k in options:
assert not ks in options, (
"Both %s and %s specified in ini file. Please use only one of "
"them, they mean thesame thing!")
options[ks] = options.pop(k)
preproc_params[ks] = options.get(ks, [[3, 3, 3], [1, 1,
1]][brain == "anat"])
# configure dartel
preproc_params['dartel'] = options.get("dartel", False)
preproc_params['output_modulated_tpms'] = options.get(
"output_modulated_tpms", False)
# can't do dartel without newsegment!
if not preproc_params["newsegment"]:
preproc_params["newsegment"] = preproc_params["dartel"]
# configure smoothing node
preproc_params["fwhm"] = options.get("fwhm", 0.)
preproc_params["anat_fwhm"] = options.get("anat_fwhm", 0.)
# how many subjects ?
subjects = []
nsubjects = options.get('nsubjects', np.inf)
exclude_these_subject_ids = options.get('exclude_these_subject_ids', [])
include_only_these_subject_ids = options.get(
'include_only_these_subject_ids', [])
def _ignore_subject(subject_id):
"""
Ignore given subject_id ?
"""
if subject_id in exclude_these_subject_ids:
return True
elif len(include_only_these_subject_ids
) and subject_id not in include_only_these_subject_ids:
return True
else:
return False
# subject data factory
subject_data_dirs = options.get("subject_dirs", "*")
if isinstance(subject_data_dirs, basestring):
subject_dir_wildcard = os.path.join(dataset_dir, subject_data_dirs)
subject_data_dirs = [
x for x in sorted(glob.glob(subject_dir_wildcard))
if os.path.isdir(x)
]
else:
# list of subjects or subject wildcards
subject_data_dirs = [
os.path.join(dataset_dir, x) for x in subject_data_dirs
]
subject_dir_wildcard = subject_data_dirs
aux = []
for subject_data_dir in subject_data_dirs:
for x in sorted(glob.glob(subject_data_dir)):
if os.path.isdir(x):
aux.append(x)
subject_data_dirs = aux
sess_func_wildcards = [
key for key in options.keys() if re.match("session_.+_func", key)
]
sess_onset_wildcards = [
key for key in options.keys() if re.match("session_.+_onset", key)
]
sess_ids = [
re.match("session_(.+)_func", session).group(1)
for session in sess_func_wildcards
]
if not subject_data_dirs:
warnings.warn("No subject directories found for wildcard: %s" %
(subject_dir_wildcard))
return [], preproc_params
for subject_data_dir in subject_data_dirs:
if len(subjects) == nsubjects:
# we've had enough subjects already; end
break
subject_id = os.path.basename(subject_data_dir)
if _ignore_subject(subject_id):
continue
subject_output_dir = os.path.join(output_dir, subject_id)
if scratch is not None:
subject_scratch = os.path.join(scratch, subject_id)
else:
subject_scratch = None
# grab functional data
func = []
sess_output_dirs = []
skip_subject = False
onset = []
for s, sess_func_wildcard in enumerate(sess_func_wildcards):
o = None
if s < len(sess_onset_wildcards):
sess_onset_wildcard = sess_onset_wildcards[s]
sess_onset_wildcard = options[sess_onset_wildcard]
sess_onset_wildcard = os.path.join(subject_data_dir,
sess_onset_wildcard)
sess_onset = sorted(glob.glob(sess_onset_wildcard))
if len(sess_onset) > 1:
raise ValueError
if len(sess_onset) > 0:
o = sess_onset[0]
onset.append(o)
sess_func_wildcard = options[sess_func_wildcard]
sess_func_wildcard = os.path.join(subject_data_dir,
sess_func_wildcard)
sess_func = sorted(glob.glob(sess_func_wildcard))
# skip session if no data found
if not sess_func:
warnings.warn(
("subject %s: No func images found for"
" wildcard %s" % (subject_id, sess_func_wildcard)))
continue
sess_dir = os.path.dirname(sess_func[0])
if len(sess_func) == 1:
sess_func = sess_func[0]
func.append(sess_func)
# session output dir
if os.path.basename(sess_dir) != os.path.basename(
subject_output_dir):
sess_output_dir = os.path.join(
subject_output_dir,
get_relative_path(subject_data_dir, sess_dir))
else:
sess_output_dir = subject_output_dir
if not os.path.exists(sess_output_dir):
os.makedirs(sess_output_dir)
sess_output_dirs.append(sess_output_dir)
# something is wrong with this guy, skip
if skip_subject:
warnings.warn("Skipping subject %s" % subject_id)
continue
# grab anat
anat = None
if not options.get("anat", None) is None:
# grap anat file(s)
anat_wildcard = os.path.join(subject_data_dir, options['anat'])
anat = glob.glob(anat_wildcard)
# skip subject if anat absent
if len(anat) < 1:
print(
"subject %s: anat image matching %s not found!; skipping"
" subject" % (subject_id, anat_wildcard))
continue
# we need just 1 anat volume
anat = anat[0]
anat_dir = os.path.dirname(anat)
else:
anat = None
anat_dir = ""
# anat output dir
anat_output_dir = None
if anat_dir:
anat_output_dir = os.path.join(
subject_output_dir,
get_relative_path(subject_data_dir, anat_dir))
if not os.path.exists(anat_output_dir):
os.makedirs(anat_output_dir)
# make subject data
subject_data = SubjectData(
subject_id=subject_id,
func=func,
anat=anat,
output_dir=subject_output_dir,
scratch=subject_scratch,
session_output_dirs=sess_output_dirs,
anat_output_dir=anat_output_dir,
session_id=sess_ids,
data_dir=subject_data_dir,
onset=onset,
TR=options.get('TR', None),
drift_model='Cosine',
hrf_model=options.get('hrf_model', 'spm + derivative'),
hfcut=options.get("hfcut", 128.),
time_units=options.get("time_units", "seconds"))
subjects.append(subject_data)
if not subjects:
warnings.warn(
"No subjects globbed (dataset_dir=%s, subject_dir_wildcard=%s" %
(dataset_dir, subject_dir_wildcard))
return subjects, preproc_params
def _generate_preproc_pipeline(config_file, dataset_dir=None, output_dir=None, options_callback=None, **kwargs):
"""
Generate pipeline (i.e subject factor + preproc params) from
config file.
dataset_dir, and output_dir can be specified in config_file, passed as
function argument, or exported in environ variables like so:
OUTPUT_DIR=/some/dir, etc.
Returns
-------
subjects: list of `SubjectData` objects
subject list
preproc_params: dict
preproc parameters
"""
# read config file
config_file = os.path.abspath(config_file)
options = _parse_job(config_file, **kwargs)
options = _del_nones_from_dict(options)
# sanitize output_dir and dataset_dir
dataset_dir = os.environ.get("DATASET_DIR", dataset_dir)
output_dir = os.environ.get("OUTPUT_DIR", output_dir)
for item in ["dataset_dir", "output_dir"]:
val = eval(item)
if val is None:
if not item in options:
# get value from environ (if exists)
val = os.environ.get(item.upper(), val)
if val is None:
raise ValueError(
(
"%s not specified (neither in environ variable, "
"nor in config_file nor in this function "
"call)"
)
% item
)
# set value from environ
if item == "dataset_dir":
dataset_dir = val
elif item == "output_dir":
output_dir = val
options["dataset_dir"] = dataset_dir = dataset_dir if not dataset_dir is None else options["dataset_dir"]
options["output_dir"] = output_dir = output_dir if not output_dir is None else options["output_dir"]
assert options["dataset_dir"]
assert options["output_dir"]
# load data from multiple dataset_dirs
if not isinstance(dataset_dir, basestring):
kwargs["output_dir"] = output_dir
tmp = [
_generate_preproc_pipeline(config_file, dataset_dir=dsd, options_callback=options_callback, **kwargs)
for dsd in dataset_dir
]
subjects = [subject for x in tmp for subject in x[0]]
return subjects, tmp[0][1]
# invoke callback
if options_callback:
options = options_callback(options)
if dataset_dir is None:
dataset_dir = options.get("dataset_dir", None)
if output_dir is None:
output_dir = options.get("output_dir", None)
# check dataset_dir
dataset_dir = _expand_path(dataset_dir)
if not os.path.isdir(dataset_dir):
raise OSError("dataset_dir %s doesn't exist" % dataset_dir)
# check output_dir
output_dir = _expand_path(options["output_dir"], relative_to=dataset_dir)
if output_dir is None:
raise OSError(
("Could not expand 'output_dir' specified in %s: invalid" " path %s (relative to directory %s)")
% (config_file, options["output_dir"], dataset_dir)
)
# dataset description
dataset_description = options.get("dataset_description", None)
# preproc parameters
preproc_params = {
"spm_dir": options.get("spm_dir", None),
"matlab_exec": options.get("matlab_exec", None),
"report": options.get("report", True),
"output_dir": output_dir,
"dataset_id": options.get("dataset_id", dataset_dir),
"n_jobs": options.get("n_jobs", None),
"caching": options.get("caching", True),
"tsdiffana": options.get("tsdiffana", True),
"dataset_description": dataset_description,
"slice_timing_software": options.get("slice_timing_software", "spm"),
"realign_software": options.get("realign_software", "spm"),
"coregister_software": options.get("coregister_software", "spm"),
"smooth_software": options.get("smooth_software", "spm"),
}
# delete orientation meta-data ?
preproc_params["deleteorient"] = options.get("deleteorient", False)
# configure slice-timing correction node
preproc_params["slice_timing"] = not options.get("disable_slice_timing", False)
# can't do STC without TR
if preproc_params["slice_timing"]:
preproc_params.update(dict((k, options.get(k, None)) for k in ["TR", "TA", "slice_order", "interleaved"]))
if preproc_params["TR"] is None:
preproc_params["slice_timing"] = False
# configure motion correction node
preproc_params["realign"] = not options.get("disable_realign", False)
if preproc_params["realign"]:
preproc_params["realign_reslice"] = options.get("reslice_realign", False)
preproc_params["register_to_mean"] = options.get("register_to_mean", True)
# configure coregistration node
preproc_params["coregister"] = not options.get("disable_coregister", False)
if preproc_params["coregister"]:
preproc_params["coregister_reslice"] = options.get("coregister_reslice")
preproc_params["coreg_anat_to_func"] = not options.get("coreg_func_to_anat", True)
# configure tissue segmentation node
preproc_params["segment"] = not options.get("disable_segment", False)
preproc_params["newsegment"] = options.get("newsegment", False) and preproc_params["segment"]
# configure normalization node
preproc_params["normalize"] = not options.get("disable_normalize", False)
# configure output voxel sizes
for brain in ["func", "anat"]:
k = "%s_write_voxel_size" % brain
ks = k + "s"
if k in options:
assert not ks in options, (
"Both %s and %s specified in ini file. Please use only one of " "them, they mean thesame thing!"
)
options[ks] = options.pop(k)
preproc_params[ks] = options.get(ks, [[3, 3, 3], [1, 1, 1]][brain == "anat"])
# configure dartel
preproc_params["dartel"] = options.get("dartel", False)
preproc_params["output_modulated_tpms"] = options.get("output_modulated_tpms", False)
# can't do dartel without newsegment!
if not preproc_params["newsegment"]:
preproc_params["newsegment"] = preproc_params["dartel"]
# configure smoothing node
preproc_params["fwhm"] = options.get("fwhm", 0.0)
preproc_params["anat_fwhm"] = options.get("anat_fwhm", 0.0)
# how many subjects ?
subjects = []
nsubjects = options.get("nsubjects", np.inf)
exclude_these_subject_ids = options.get("exclude_these_subject_ids", [])
include_only_these_subject_ids = options.get("include_only_these_subject_ids", [])
def _ignore_subject(subject_id):
"""
Ignore given subject_id ?
"""
if subject_id in exclude_these_subject_ids:
return True
elif len(include_only_these_subject_ids) and not subject_id in include_only_these_subject_ids:
return True
else:
return False
# subject data factory
subject_dir_wildcard = os.path.join(dataset_dir, options.get("subject_dirs", "*"))
sess_func_wildcards = [k for k in options.keys() if re.match("session_.+_func", k)]
sess_onset_wildcards = [k for k in options.keys() if re.match("session_.+_onset", k)]
sess_ids = [re.match("session_(.+)_func", session).group(1) for session in sess_func_wildcards]
subject_data_dirs = [x for x in sorted(glob.glob(subject_dir_wildcard)) if os.path.isdir(x)]
if not subject_data_dirs:
warnings.warn("No subject directories found for wildcard: %s" % (subject_dir_wildcard))
return [], preproc_params
for subject_data_dir in subject_data_dirs:
if len(subjects) == nsubjects:
# we've had enough subjects already; end
break
subject_id = os.path.basename(subject_data_dir)
if _ignore_subject(subject_id):
continue
subject_output_dir = os.path.join(output_dir, subject_id)
# grab functional data
func = []
sess_output_dirs = []
skip_subject = False
onset = []
for s, sess_func_wildcard in enumerate(sess_func_wildcards):
o = None
if s < len(sess_onset_wildcards):
sess_onset_wildcard = sess_onset_wildcards[s]
sess_onset_wildcard = options[sess_onset_wildcard]
sess_onset_wildcard = os.path.join(subject_data_dir, sess_onset_wildcard)
sess_onset = sorted(glob.glob(sess_onset_wildcard))
if len(sess_onset) > 1:
raise ValueError
if len(sess_onset) > 0:
o = sess_onset[0]
onset.append(o)
sess_func_wildcard = options[sess_func_wildcard]
sess_func_wildcard = os.path.join(subject_data_dir, sess_func_wildcard)
sess_func = sorted(glob.glob(sess_func_wildcard))
# skip session if no data found
if not sess_func:
warnings.warn(
("subject %s: No func images found for" " wildcard %s" % (subject_id, sess_func_wildcard))
)
continue
sess_dir = os.path.dirname(sess_func[0])
if len(sess_func) == 1:
sess_func = sess_func[0]
func.append(sess_func)
# session output dir
if os.path.basename(sess_dir) != os.path.basename(subject_output_dir):
sess_output_dir = os.path.join(subject_output_dir, get_relative_path(subject_data_dir, sess_dir))
else:
sess_output_dir = subject_output_dir
if not os.path.exists(sess_output_dir):
os.makedirs(sess_output_dir)
sess_output_dirs.append(sess_output_dir)
# something is wrong with this guy, skip
if skip_subject:
warnings.warn("Skipping subject %s" % subject_id)
continue
# grab anat
anat = None
if not options.get("anat", None) is None:
# grap anat file(s)
anat_wildcard = os.path.join(subject_data_dir, options["anat"])
anat = glob.glob(anat_wildcard)
# skip subject if anat absent
if len(anat) < 1:
print (
"subject %s: anat image matching %s not found!; skipping" " subject" % (subject_id, anat_wildcard)
)
continue
# we need just 1 anat volume
anat = anat[0]
anat_dir = os.path.dirname(anat)
else:
anat = None
anat_dir = ""
# anat output dir
anat_output_dir = None
if anat_dir:
anat_output_dir = os.path.join(subject_output_dir, get_relative_path(subject_data_dir, anat_dir))
if not os.path.exists(anat_output_dir):
os.makedirs(anat_output_dir)
# make subject data
subject_data = SubjectData(
subject_id=subject_id,
func=func,
anat=anat,
output_dir=subject_output_dir,
session_output_dirs=sess_output_dirs,
anat_output_dir=anat_output_dir,
session_id=sess_ids,
data_dir=subject_data_dir,
onset=onset,
TR=options.get("TR", None),
drift_model="Cosine",
hrf_model=options.get("hrf_model", "Canonical With Derivative"),
hfcut=options.get("hfcut", 128.0),
time_units=options.get("time_units", "seconds"),
)
subjects.append(subject_data)
if not subjects:
warnings.warn(
"No subjects globbed (dataset_dir=%s, subject_dir_wildcard=%s" % (dataset_dir, subject_dir_wildcard)
)
return subjects, preproc_params
def _generate_preproc_pipeline(jobfile,
dataset_dir=None,
options_callback=None,
**kwargs):
"""
Generate pipeline (i.e subject factor + preproc params) from
config file.
Returns
-------
subjects: list of `SubjectData` objects
subject list
preproc_params: dict
preproc parameters
"""
# read config file
jobfile = os.path.abspath(jobfile)
options = _parse_job(jobfile, **kwargs)
options = _del_nones_from_dict(options)
# generate subject conf
if dataset_dir is None:
assert "dataset_dir" in options, (
"dataset_dir not specified (neither in jobfile"
" nor in this function call)")
dataset_dir = options["dataset_dir"]
else:
assert not dataset_dir is None, (
"dataset_dir not specified (neither in jobfile"
" nor in this function call")
options["dataset_dir"] = dataset_dir
if not isinstance(dataset_dir, basestring):
tmp = [
_generate_preproc_pipeline(jobfile,
dataset_dir=dsd,
options_callback=options_callback,
**kwargs) for dsd in dataset_dir
]
subjects = [subject for x in tmp for subject in x[0]]
return subjects, tmp[0][1]
if options_callback:
options = options_callback(options)
dataset_dir = options["dataset_dir"]
dataset_dir = _expand_path(dataset_dir)
assert os.path.isdir(dataset_dir), ("dataset_dir %s doesn't exist" %
dataset_dir)
# output dir
output_dir = _expand_path(options["output_dir"], relative_to=dataset_dir)
if output_dir is None:
raise RuntimeError(
("Could not expand 'output_dir' specified in %s: invalid"
" path %s (relative to directory %s)") %
(jobfile, options["output_dir"], dataset_dir))
# dataset description
dataset_description = options.get("dataset_description", None)
# preproc parameters
preproc_params = {
"spm_dir": options.get("spm_dir", None),
"matlab_exec": options.get("matlab_exec", None),
"report": options.get("report", True),
"output_dir": output_dir,
"dataset_id": options.get("dataset_id", dataset_dir),
"n_jobs": options.get("n_jobs", None),
"caching": options.get("caching", True),
"cv_tc": options.get("cv_tc", True),
"dataset_description": dataset_description,
"slice_timing_software": options.get("slice_timing_software", "spm"),
"realign_software": options.get("realign_software", "spm"),
"coregister_software": options.get("coregister_software", "spm"),
}
# delete orientation meta-data ?
preproc_params['deleteorient'] = options.get("deleteorient", False)
# configure slice-timing correction node
preproc_params["slice_timing"] = not options.get("disable_slice_timing",
False)
# can't do STC without TR
if preproc_params["slice_timing"]:
preproc_params.update(
dict((k, options.get(k, None))
for k in ["TR", "TA", "slice_order", "interleaved"]))
if preproc_params["TR"] is None:
preproc_params["slice_timing"] = False
# configure motion correction node
preproc_params["realign"] = not options.get("disable_realign", False)
if preproc_params["realign"]:
preproc_params['realign_reslice'] = options.get(
"reslice_realign", False)
preproc_params['register_to_mean'] = options.get(
"register_to_mean", True)
# configure coregistration node
preproc_params["coregister"] = not options.get("disable_coregister", False)
if preproc_params["coregister"]:
preproc_params['coregister_reslice'] = options["coregister_reslice"]
preproc_params['coreg_anat_to_func'] = not options.get(
"coreg_func_to_anat", True)
# configure tissue segmentation node
preproc_params["segment"] = not options.get("disable_segment", False)
if preproc_params["segment"]:
pass # XXX pending code...
# configure normalization node
preproc_params["normalize"] = not options.get("disable_normalize", False)
# configure output voxel sizes
for brain in ["func", "anat"]:
k = "%s_write_voxel_size" % brain
ks = k + "s"
if k in options:
assert not ks in options, (
"Both %s and %s specified in ini file. Please use only one of "
"them, they mean thesame thing!")
options[ks] = options.pop(k)
else:
print k
preproc_params[ks] = options.get(ks, [[3, 3, 3], [1, 1,
1]][brain == "anat"])
# configure dartel
preproc_params['dartel'] = options.get("dartel", False)
preproc_params['output_modulated_tpms'] = options.get(
"output_modulated_tpms", False)
# configure smoothing node
preproc_params["fwhm"] = options.get("fwhm", 0.)
preproc_params["anat_fwhm"] = options.get("anat_fwhm", 0.)
# how many subjects ?
subjects = []
nsubjects = options.get('nsubjects', np.inf)
exclude_these_subject_ids = options.get('exclude_these_subject_ids', [])
include_only_these_subject_ids = options.get(
'include_only_these_subject_ids', [])
def _ignore_subject(subject_id):
"""
Ignore given subject_id ?
"""
if subject_id in exclude_these_subject_ids: return True
elif len(include_only_these_subject_ids
) and not subject_id in include_only_these_subject_ids:
return True
else:
return False
# subject data factory
subject_dir_wildcard = os.path.join(dataset_dir,
options.get("subject_dirs", "*"))
sessions = [k for k in options.keys() if re.match("session_.+_func", k)]
session_ids = [
re.match("session_(.+)_func", session).group(1) for session in sessions
]
subject_data_dirs = sorted(glob.glob(subject_dir_wildcard))
if not subject_data_dirs:
warnings.warn("No subject directories found for wildcard: %s" %
(subject_dir_wildcard))
return [], preproc_params
for subject_data_dir in subject_data_dirs:
if len(subjects) == nsubjects: break
subject_id = os.path.basename(subject_data_dir)
if _ignore_subject(subject_id): continue
subject_output_dir = os.path.join(output_dir, subject_id)
# grab functional data
func = []
sess_output_dirs = []
skip_subject = False
for session in sessions:
session = options[session]
sess_func_wildcard = os.path.join(subject_data_dir, session)
sess_func = sorted(glob.glob(sess_func_wildcard))
if not sess_func:
print("subject %s: No func images found for"
" wildcard %s" % (subject_id, sess_func_wildcard))
skip_subject = True
break
sess_dir = os.path.dirname(sess_func[0])
if len(sess_func) == 1:
sess_func = sess_func[0]
func.append(sess_func)
# session output dir
if os.path.basename(sess_dir) != os.path.basename(
subject_output_dir):
sess_output_dir = os.path.join(
subject_output_dir,
get_relative_path(subject_data_dir, sess_dir))
else:
sess_output_dir = subject_output_dir
if not os.path.exists(sess_output_dir):
os.makedirs(sess_output_dir)
sess_output_dirs.append(sess_output_dir)
if skip_subject:
print "Skipping subject %s" % subject_id
continue
# grab anat
anat = None
if not options.get("anat", None) is None:
anat_wildcard = os.path.join(subject_data_dir, options['anat'])
anat = glob.glob(anat_wildcard)
# skip subject if anat absent
if len(anat) < 1:
print(
"subject %s: anat image matching %s not found!; skipping"
" subject" % (subject_id, anat_wildcard))
continue
anat = anat[0]
anat_dir = os.path.dirname(anat)
else:
anat = None
anat_dir = ""
# anat output dir
anat_output_dir = None
if anat_dir:
anat_output_dir = os.path.join(
subject_output_dir,
get_relative_path(subject_data_dir, anat_dir))
if not os.path.exists(anat_output_dir):
os.makedirs(anat_output_dir)
# make subject data
subject_data = SubjectData(subject_id=subject_id,
func=func,
anat=anat,
output_dir=subject_output_dir,
session_output_dirs=sess_output_dirs,
anat_output_dir=anat_output_dir,
session_id=session_ids,
data_dir=subject_data_dir)
subjects.append(subject_data)
if not subjects:
warnings.warn(
"No subjects globbed (dataset_dir=%s, subject_dir_wildcard=%s" %
(dataset_dir, subject_dir_wildcard))
return subjects, preproc_params
def configure_spm(matlab_exec=None, spm_dir=None):
# configure MATLAB
if 'MATLAB_EXEC' in os.environ:
matlab_exec = os.environ['MATLAB_EXEC']
# use SPM_MCR defined by environment variable
if (distutils.version.LooseVersion(nipype.__version__).version >= [0, 9]
and 'SPM_MCR' in os.environ
and os.path.exists(os.environ['SPM_MCR'])):
spm_dir = os.environ['SPM_DIR']
matlab_cmd = '%s run script' % os.environ['SPM_MCR']
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
# use hard coded SPM_MCR
elif (distutils.version.LooseVersion(nipype.__version__).version >= [0, 9]
and os.path.exists('/i2bm/local/bin/spm8')):
spm_dir = '/i2bm/local/spm8-standalone/spm8_mcr/spm8'
matlab_cmd = '/i2bm/local/bin/spm8 run script'
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
# use Matlab with SPM toolbox
else:
# try real hard to find matlab only if not using the mcr
if not matlab_exec is None:
matlab_exec = _expand_path(matlab_exec)
if matlab_exec is None or not os.path.exists(matlab_exec):
if matlab_exec:
print "Path %s doesn't exist" % matlab_exec
matlab_exec = DEFAULT_MATLAB_EXEC
if not os.path.exists(matlab_exec):
m_choices = glob.glob("/neurospin/local/matlab/R*/bin/matlab")
if m_choices:
matlab_exec = m_choices[0]
assert os.path.exists(matlab_exec), (
"Can't find matlab path: '%s' ! You should export MATLAB_EXEC="
"/path/to/your/matlab/exec, doesn't exist; you need to export "
"matlab_exec" % matlab_exec)
matlab.MatlabCommand.set_default_matlab_cmd(matlab_exec)
# configure SPM
if 'SPM_DIR' in os.environ and spm_dir is None:
spm_dir = os.environ['SPM_DIR']
if not spm_dir is None:
spm_dir = _expand_path(spm_dir)
if spm_dir is None or not os.path.isdir(spm_dir):
if spm_dir:
print "Path %s doesn't exist" % spm_dir
print "spm_dir defaulting to %s" % DEFAULT_SPM_DIR
spm_dir = DEFAULT_SPM_DIR
assert os.path.exists(spm_dir), (
"Can't find SPM path '%s'! You should export SPM_DIR=/path/to/"
"your/SPM/root/dir" % spm_dir)
matlab.MatlabCommand.set_default_paths(spm_dir)
return spm_dir, matlab_exec