def subject_factory():
"""
Producer for HAXBY subject data.
"""
for subject_id in set(
[os.path.basename(os.path.dirname(x)) for x in haxby_data.func]):
# instantiate subject_data object
subject_data = SubjectData()
subject_data.subject_id = subject_id
subject_data.session_id = "haxby2001"
# set func
subject_data.func = [x for x in haxby_data.func if subject_id in x]
assert len(subject_data.func) == 1
subject_data.func = subject_data.func[0]
# set anat
subject_data.anat = [x for x in haxby_data.func if subject_id in x]
assert len(subject_data.anat) == 1
subject_data.anat = subject_data.anat[0]
# set subject output directory
subject_data.output_dir = os.path.join(OUTPUT_DIR,
subject_data.subject_id)
yield subject_data
def _nyu_rest_factory(session=1):
from pypreprocess.nipype_preproc_spm_utils import SubjectData
nyu_data = fetch_nyu_rest(sessions=[session], n_subjects=7)
session_func = [x for x in nyu_data.func if "session%i" % session in x]
session_anat = [
x for x in nyu_data.anat_skull if "session%i" % session in x]
for subject_id in set([os.path.basename(os.path.dirname
(os.path.dirname(x)))
for x in session_func]):
# instantiate subject_data object
subject_data = SubjectData()
subject_data.subject_id = subject_id
subject_data.session_id = session
# set func
subject_data.func = [x for x in session_func if subject_id in x]
assert len(subject_data.func) == 1
subject_data.func = subject_data.func[0]
# set anat
subject_data.anat = [x for x in session_anat if subject_id in x]
assert len(subject_data.anat) == 1
subject_data.anat = subject_data.anat[0]
# set subject output directory
subject_data.output_dir = "/tmp/%s" % subject_id
subject_data.sanitize(deleteorient=True, niigz2nii=False)
yield (subject_data.subject_id, subject_data.func[0],
subject_data.anat)
def subject_factory():
"""
Producer for HAXBY subject data.
"""
for subject_id in set([os.path.basename(
os.path.dirname(x))
for x in haxby_data.func]):
# instantiate subject_data object
subject_data = SubjectData()
subject_data.subject_id = subject_id
subject_data.session_id = "haxby2001"
# set func
subject_data.func = [x for x in haxby_data.func if subject_id in x]
assert len(subject_data.func) == 1
subject_data.func = subject_data.func[0]
# set anat
subject_data.anat = [x for x in haxby_data.func if subject_id in x]
assert len(subject_data.anat) == 1
subject_data.anat = subject_data.anat[0]
# set subject output directory
subject_data.output_dir = os.path.join(OUTPUT_DIR,
subject_data.subject_id)
yield subject_data
def _nyu_rest_factory(session=1):
from pypreprocess.nipype_preproc_spm_utils import SubjectData
nyu_data = fetch_nyu_rest(sessions=[session], n_subjects=7)
session_func = [x for x in nyu_data.func if "session%i" % session in x]
session_anat = [
x for x in nyu_data.anat_skull if "session%i" % session in x]
for subject_id in set([os.path.basename(os.path.dirname
(os.path.dirname(x)))
for x in session_func]):
# instantiate subject_data object
subject_data = SubjectData()
subject_data.subject_id = subject_id
subject_data.session_id = session
# set func
subject_data.func = [x for x in session_func if subject_id in x]
assert len(subject_data.func) == 1
subject_data.func = subject_data.func[0]
# set anat
subject_data.anat = [x for x in session_anat if subject_id in x]
assert len(subject_data.anat) == 1
subject_data.anat = subject_data.anat[0]
# set subject output directory
subject_data.output_dir = "/tmp/%s" % subject_id
subject_data.sanitize(deleteorient=True, niigz2nii=False)
yield (subject_data.subject_id, subject_data.func[0],
subject_data.anat)
def subject_factory():
for subject_id in subject_ids:
if subject_id in exclusions:
continue
# construct subject data structure
subject_data = SubjectData()
subject_data.session_id = session_ids
subject_data.subject_id = subject_id
subject_data.func = []
# glob for bold data
has_bad_sessions = False
for session_id in subject_data.session_id:
bold_dir = os.path.join(
data_dir,
"%s/BOLD/%s" % (subject_id, session_id))
# # extract .nii.gz to .nii
# unzip_nii_gz(bold_dir)
# glob bold data for this session
func = glob.glob(os.path.join(bold_dir, "bold.nii.gz"))
# check that this session is OK (has bold data, etc.)
if not func:
has_bad_sessions = True
break
subject_data.func.append(func[0])
# exclude subject if necessary
if has_bad_sessions:
continue
# glob for anatomical data
# anat_dir = os.path.join(
# data_dir,
# "%s/anatomy" % subject_id)
# # extract .nii.gz to .ni
# unzip_nii_gz(anat_dir)
# glob anatomical data proper
subject_data.anat = glob.glob(
os.path.join(
data_dir,
"%s/anatomy/highres001_brain.nii.gz" % subject_id))[0]
# set subject output dir (all calculations for
# this subject go here)
subject_data.output_dir = os.path.join(
output_dir,
subject_id)
yield subject_data
N_SUBJECTS = 2
haxby_data = fetch_haxby(n_subjects=N_SUBJECTS)
# set output dir
OUTPUT_DIR = os.path.join(os.path.dirname(haxby_data.mask), "haxby_runs")
if not os.path.exists(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR)
# get subject data
subjects = []
for subject_id in set(
[os.path.basename(os.path.dirname(x)) for x in haxby_data.func]):
# instantiate subject_data object
subject_data = SubjectData()
subject_data.subject_id = subject_id
subject_data.session_id = "haxby2001"
# set func
subject_data.func = [x for x in haxby_data.func if subject_id in x]
assert len(subject_data.func) == 1
subject_data.func = subject_data.func[0]
# set anat
subject_data.anat = [x for x in haxby_data.anat if subject_id in x]
assert len(subject_data.anat) == 1
subject_data.anat = subject_data.anat[0]
# set subject output directory
subject_data.output_dir = os.path.join(OUTPUT_DIR, subject_data.subject_id)
haxby_data = fetch_haxby(n_subjects=N_SUBJECTS)
# set output dir
OUTPUT_DIR = os.path.join(os.path.dirname(haxby_data.mask),
"haxby_runs")
if not os.path.exists(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR)
# get subject data
subjects = []
for subject_id in set([os.path.basename(os.path.dirname(x))
for x in haxby_data.func]):
# instantiate subject_data object
subject_data = SubjectData()
subject_data.subject_id = subject_id
subject_data.session_id = "haxby2001"
# set func
subject_data.func = [x for x in haxby_data.func if subject_id in x]
assert len(subject_data.func) == 1
subject_data.func = subject_data.func[0]
# set anat
subject_data.anat = [x for x in haxby_data.anat if subject_id in x]
assert len(subject_data.anat) == 1
subject_data.anat = subject_data.anat[0]
# set subject output directory
subject_data.output_dir = os.path.join(OUTPUT_DIR,
subject_data.subject_id)