def execute_glms(docs, out_dir, contrast_definitions=None,
outputs=None, glm_model='ar1', dataset_id=None,
do_preproc=True,
smoothed=None,
n_jobs=None):
"""Function to execute a series of GLMs (one per subject)
"""
# sanity
n_jobs = len(docs)
n_jobs = min(n_jobs, multiprocessing.cpu_count() / 4)
# preprocess the data
if do_preproc:
if not smoothed is None:
fwhm = smoothed
else:
fwhm = smoothed
subject_fmri_perms = {}
def subject_factory():
for doc in docs:
subject_data = SubjectData()
subject_data.subject_id = doc['subject']
# grap anat filename like a ninja
subject_data.anat = os.path.join(
re.search(
".+?%s\/fMRI\/acquisition1" % subject_data.subject_id,
doc['raw_data'][0]).group().replace("fMRI", "t1mri"),
"anat_%s_3T_neurospin.img" % subject_data.subject_id)
# don't want no ugly supprises hereafter
assert os.path.exists(subject_data.anat)
# grab subject session ids like a ninja
subject_data.session_id = sorted(list(set(
[re.search("\/acquisition1\/(.+?)\/",
x).group(1)
for x in doc['raw_data']])))
# collect list of lists of 3D scans (one list per session)
perm = []
subject_data.func = [sorted(
[x for x in doc['raw_data'] if s in x])
for s in subject_data.session_id]
_tmp = [x for session_fmri_files in subject_data.func
for x in session_fmri_files]
for fmri_filename in doc['raw_data']:
for k in range(len(_tmp)):
if fmri_filename == _tmp[k]:
perm.append(k)
break
subject_fmri_perms[subject_data.subject_id] = perm
# set subject output directory (so there'll be no pollution)
subject_data.output_dir = os.path.join(
out_dir, subject_data.subject_id)
if not os.path.exists(subject_data.output_dir):
os.makedirs(subject_data.output_dir)
# yield input data for this subject
yield subject_data
preproc_results = do_subjects_preproc(
subject_factory(),
output_dir=out_dir,
dataset_id=dataset_id,
fwhm=fwhm,
n_jobs=n_jobs,
# do_report=False,
)
# sanitize
assert len(preproc_results) == len(docs)
for doc in docs:
for preproc_result in preproc_results:
if preproc_result['subject_id'] == doc['subject']:
# fix shuffled (due to sorting in preproc pipeline)
# session-wise fmri files, lest activation maps will be
# ultimate garbage
doc['data'] = list(np.array([
x for session_fmri_files in preproc_result['func']
for x in session_fmri_files])[
subject_fmri_perms[doc['subject']]])
break
# execute one GLM per subject
if do_preproc:
output_dir = out_dir
else:
output_dir = os.path.join(out_dir, "not_repreprocessed")
joblib.Parallel(n_jobs=max(n_jobs / 4, 1))(joblib.delayed(execute_glm)(
doc,
output_dir,
contrast_definitions,
outputs,
glm_model,
) for doc in docs)
"""fetch input data"""
_subject_data = fetch_fsl_feeds_data(data_dir)
subject_data = nipype_preproc_spm_utils.SubjectData()
subject_data.subject_id = "sub001"
subject_data.func = _subject_data["func"]
unzip_nii_gz(os.path.dirname(subject_data.func))
subject_data.anat = _subject_data["anat"]
subject_data.output_dir = os.path.join(
output_dir, subject_data.subject_id)
unzip_nii_gz(os.path.dirname(subject_data.anat))
"""preprocess the data"""
results = nipype_preproc_spm_utils.do_subjects_preproc(
[subject_data],
output_dir=output_dir,
# fwhm=[5, 5, 5],
dataset_id="FSL FEEDS single-subject",
dataset_description=DATASET_DESCRIPTION,
do_shutdown_reloaders=False,
)
"""collect preprocessed data"""
fmri_files = results[0]['func']
anat_file = results[0]['anat']
"""specify contrasts"""
contrasts = {}
n_columns = len(design_matrix.names)
I = np.eye(len(design_matrix.names))
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = I[2 * i]
data_dir=DATA_DIR,
subject_ids=subject_ids,
n_jobs=len(subject_ids))
def subject_factory():
"""producer for subject (input) data"""
for subject_id, sd in haxby_data.iteritems():
subject_data = nipype_preproc_spm_utils.SubjectData()
subject_data.session_id = "haxby2001"
subject_data.subject_id = subject_id
unzip_nii_gz(sd.subject_dir)
subject_data.anat = sd.anat.replace(".gz", "")
subject_data.func = sd.bold.replace(".gz", "")
subject_data.output_dir = os.path.join(
OUTPUT_DIR, subject_data.subject_id)
yield subject_data
"""do preprocessing proper"""
results = nipype_preproc_spm_utils.do_subjects_preproc(
subject_factory(),
output_dir=OUTPUT_DIR,
dataset_id="HAXBY 2001",
do_realign=False,
do_coreg=False,
do_dartel=DO_DARTEL,
do_cv_tc=False,
dataset_description=DATASET_DESCRIPTION,
)
def preproc_abide_institute(institute_id, abide_data_dir, abide_output_dir,
do_dartel=True,
do_report=True,
n_jobs=-1,
):
"""Preprocesses a given ABIDE institute
"""
# set institute output dir
institute_output_dir = os.path.join(abide_output_dir, institute_id)
if not os.path.exists(institute_output_dir):
os.makedirs(institute_output_dir)
# set subject id wildcard for globbing institute subjects
subject_id_wildcard = "%s_*/%s_*" % (institute_id, institute_id)
# glob for subject ids
subject_ids = [os.path.basename(x)
for x in glob.glob(os.path.join(abide_data_dir,
subject_id_wildcard))]
# sort the ids
subject_ids.sort()
ignored_subject_ids = []
# producer subject data
def subject_factory():
for subject_id in subject_ids:
subject_data = nipype_preproc_spm_utils.SubjectData()
subject_data.subject_id = subject_id
try:
subject_data.func = glob.glob(
os.path.join(
abide_data_dir,
"%s/%s/scans/rest*/resources/NIfTI/files/rest.nii" % (
subject_id, subject_id)))[0]
except IndexError:
ignored_because = "no rest data found"
print "Ignoring subject %s (%s)" % (subject_id,
ignored_because)
ignored_subject_ids.append((subject_id, ignored_because))
continue
try:
subject_data.anat = glob.glob(
os.path.join(
abide_data_dir,
"%s/%s/scans/anat/resources/NIfTI/files/mprage.nii" % (
subject_id, subject_id)))[0]
except IndexError:
if do_dartel:
# can't do DARTEL in under such conditions
continue
try:
subject_data.hires = glob.glob(
os.path.join(
abide_data_dir,
("%s/%s/scans/hires/resources/NIfTI/"
"files/hires.nii") % (subject_id, subject_id)))[0]
except IndexError:
ignored_because = "no anat/hires data found"
print "Ignoring subject %s (%s)" % (subject_id,
ignored_because)
ignored_subject_ids.append((subject_id, ignored_because))
continue
subject_data.output_dir = os.path.join(
os.path.join(
institute_output_dir, subject_id))
yield subject_data
# do preprocessing proper
report_filename = os.path.join(institute_output_dir,
"_report.html")
nipype_preproc_spm_utils.do_subjects_preproc(
subject_factory(),
dataset_id=institute_id,
output_dir=institute_output_dir,
do_report=do_report,
do_dartel=do_dartel,
dataset_description="%s" % DATASET_DESCRIPTION.replace(
"%s",
institute_id),
report_filename=report_filename,
do_shutdown_reloaders=True,)
for subject_id, ignored_because in ignored_subject_ids:
print "Ignored %s because %s" % (subject_id, ignored_because)
def dataset_preprocessing(dataset_id, data_dir, output_dir, ignore_list=None,
dataset_description=None):
"""Main function for preprocessing (and analysis ?)
Parameters
----------
returns list of Bunch objects with fields anat, func, and subject_id
for each preprocessed subject
"""
data_dir = os.path.join(data_dir, dataset_id)
if not os.path.exists(data_dir):
os.makedirs(data_dir)
output_dir = os.path.join(output_dir, dataset_id)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
dataset_description = DATASET_DESCRIPTION if \
dataset_description is None else dataset_description
ignore_list = [] if ignore_list is None else ignore_list
# glob for subject ids
subjects_id = [
os.path.basename(x)
for x in glob.glob(os.path.join(data_dir, subject_id_wildcard))]
subjects_id.sort()
sessions_id = {}
# producer subject data
def subject_factory():
for subject_id in subjects_id:
if subject_id in ignore_list:
continue
sessions = get_subject_sessions(os.path.join(data_dir, subject_id))
sessions_id[subject_id] = sessions
# construct subject data structure
subject_data = nipype_preproc_spm_utils.SubjectData()
subject_data.session_id = sessions
subject_data.subject_id = subject_id
subject_data.func = []
assert sessions != []
# 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"))
# 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" % 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
# do preprocessing proper
report_filename = os.path.join(output_dir, "_report.html")
for results in nipype_preproc_spm_utils.do_subjects_preproc(
subject_factory(),
n_jobs=1,
output_dir=output_dir,
do_deleteorient=True, # some openfmri data have garbage orientation
do_dartel=DO_DARTEL,
dataset_id=dataset_id,
# do_cv_tc=False,
dataset_description=dataset_description,
# do_report=False,
report_filename=report_filename,
do_shutdown_reloaders=True, # XXX rm this if u want to chain GLM QA
):
pass
subject_id = results['subject_id']
# dump results in openfmri layout
if not isinstance(results['estimated_motion'], list):
results['estimated_motion'] = [results['estimated_motion']]
if not isinstance(results['func'], list):
results['func'] = [results['func']]
img = nb.load(results['anat'])
nb.save(img, os.path.join(
data_dir, subject_id, 'anatomy',
'normalized_highres001.nii.gz'))
for session_id, motion, func in zip(sessions_id[subject_id],
results['estimated_motion'],
results['func']):
# estimated motion
shutil.copyfile(motion, os.path.join(
data_dir, subject_id, 'BOLD', session_id, 'motion.txt'))
# preprocessed bold
img = nb.load(func)
nb.save(img, os.path.join(
data_dir, subject_id, 'BOLD',
session_id, 'normalized_bold.nii.gz'))
import reporting.glm_reporter as glm_reporter
DATA_DIR = "/home/elvis/Downloads/alex_spm/"
OUTPUT_DIR = "spm_multimodal_runs"
# fetch the data
subject_data = nipype_preproc_spm_utils.SubjectData()
subject_data.subject_id = "sub001"
subject_data.session_id = ["Session1", "Session2"]
subject_data.func = [sorted(glob.glob(os.path.join(
DATA_DIR,
"fMRI/%s/fMETHODS-*.img" % s)))
for s in subject_data.session_id]
subject_data.anat = os.path.join(DATA_DIR, "sMRI/smri.img")
subject_data.output_dir = os.path.join(OUTPUT_DIR,
subject_data.subject_id)
"""preprocess the data"""
results = nipype_preproc_spm_utils.do_subjects_preproc(
[subject_data],
output_dir=OUTPUT_DIR,
fwhm=[8, 8, 8],
dataset_id="SPM MULTIMODAL (see @alex)",
do_shutdown_reloaders=False,
)
# set anat
subject_data.anat = [
x.replace(".gz", "") for x in session_anat if subject_id in x]
assert len(subject_data.anat) == 1
subject_data.anat = subject_data.anat[0]
unzip_nii_gz(os.path.dirname(subject_data.anat))
# set subject output directory
subject_data.output_dir = os.path.join(
session_output_dir, subject_data.subject_id)
yield subject_data
# do preprocessing proper
for session in SESSIONS:
session_output_dir = os.path.join(OUTPUT_DIR, "session%i" % session)
# preproprec this session for all subjects
print ("\r\n\r\n\t\t\tPreprocessing session %i for all subjects..."
"\r\n\r\n") % session
nipype_preproc_spm_utils.do_subjects_preproc(
subject_factory(session_output_dir, session),
output_dir=session_output_dir,
do_deleteorient=True,
do_dartel=DARTEL,
dataset_id="NYU Test Rest session %i" % session,
dataset_description=DATASET_DESCRIPTION,
)
print "Done (NYU Test Rest preprocessing)"
def main(data_dir, output_dir, exclusions=None, dataset_id=None):
"""Main function for preprocessing (and analysis ?)
Parameters
----------
returns list of Bunch objects with fields anat, func, and subject_id
for each preprocessed subject
"""
exclusions = [] if exclusions is None else exclusions
# glob for subject ids
subject_ids = [
os.path.basename(x)
for x in glob.glob(os.path.join(data_dir, subject_id_wildcard))]
model_dirs = glob.glob(os.path.join(
data_dir, subject_ids[0], 'model', '*'))
session_ids = [
os.path.basename(x)
for x in glob.glob(os.path.join(model_dirs[0], 'onsets', '*'))]
session_ids.sort()
subject_ids.sort()
# producer subject data
def subject_factory():
for subject_id in subject_ids:
if subject_id in exclusions:
continue
# construct subject data structure
subject_data = nipype_preproc_spm_utils.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"))
# 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" % 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
# do preprocessing proper
report_filename = os.path.join(output_dir,
"_report.html")
return nipype_preproc_spm_utils.do_subjects_preproc(
subject_factory(),
dataset_id=dataset_id,
output_dir=output_dir,
do_deleteorient=True, # some openfmri data have garbage orientation
do_dartel=DO_DARTEL,
# do_cv_tc=False,
dataset_description=DATASET_DESCRIPTION,
report_filename=report_filename,
do_shutdown_reloaders=True
)
"""fetch spm auditory data"""
_subject_data = fetch_spm_auditory_data(DATA_DIR)
subject_data = nipype_preproc_spm_utils.SubjectData()
subject_data.subject_id = "sub001"
subject_data.func = _subject_data["func"]
subject_data.anat = _subject_data["anat"]
subject_data.output_dir = os.path.join(
OUTPUT_DIR, subject_data.subject_id)
print subject_data.func
"""preprocess the data"""
results = nipype_preproc_spm_utils.do_subjects_preproc(
[subject_data],
output_dir=OUTPUT_DIR,
dataset_id="SPM single-subject auditory",
dataset_description=DATASET_DESCRIPTION,
do_shutdown_reloaders=False,
)
"""collect preprocessed data"""
"""collect preprocessed data"""
fmri_files = results[0]['func']
anat_file = results[0]['anat']
import nibabel as ni
if isinstance(fmri_files, basestring):
fmri_img = ni.load(fmri_files)
else:
output_filename = '/tmp/spm_auditory.nii.gz'
def execute_glms(docs,
out_dir,
contrast_definitions=None,
outputs=None,
glm_model='ar1',
dataset_id=None,
do_preproc=True,
smoothed=None,
n_jobs=None):
"""Function to execute a series of GLMs (one per subject)
"""
# sanity
n_jobs = len(docs)
n_jobs = min(n_jobs, multiprocessing.cpu_count() / 4)
# preprocess the data
if do_preproc:
if not smoothed is None:
fwhm = smoothed
else:
fwhm = smoothed
subject_fmri_perms = {}
def subject_factory():
for doc in docs:
subject_data = SubjectData()
subject_data.subject_id = doc['subject']
# grap anat filename like a ninja
subject_data.anat = os.path.join(
re.search(
".+?%s\/fMRI\/acquisition1" % subject_data.subject_id,
doc['raw_data'][0]).group().replace("fMRI", "t1mri"),
"anat_%s_3T_neurospin.img" % subject_data.subject_id)
# don't want no ugly supprises hereafter
assert os.path.exists(subject_data.anat)
# grab subject session ids like a ninja
subject_data.session_id = sorted(
list(
set([
re.search("\/acquisition1\/(.+?)\/", x).group(1)
for x in doc['raw_data']
])))
# collect list of lists of 3D scans (one list per session)
perm = []
subject_data.func = [
sorted([x for x in doc['raw_data'] if s in x])
for s in subject_data.session_id
]
_tmp = [
x for session_fmri_files in subject_data.func
for x in session_fmri_files
]
for fmri_filename in doc['raw_data']:
for k in xrange(len(_tmp)):
if fmri_filename == _tmp[k]:
perm.append(k)
break
subject_fmri_perms[subject_data.subject_id] = perm
# set subject output directory (so there'll be no pollution)
subject_data.output_dir = os.path.join(out_dir,
subject_data.subject_id)
if not os.path.exists(subject_data.output_dir):
os.makedirs(subject_data.output_dir)
# yield input data for this subject
yield subject_data
preproc_results = do_subjects_preproc(
subject_factory(),
output_dir=out_dir,
dataset_id=dataset_id,
fwhm=fwhm,
n_jobs=n_jobs,
# do_report=False,
)
# sanitize
assert len(preproc_results) == len(docs)
for doc in docs:
for preproc_result in preproc_results:
if preproc_result['subject_id'] == doc['subject']:
# fix shuffled (due to sorting in preproc pipeline)
# session-wise fmri files, lest activation maps will be
# ultimate garbage
doc['data'] = list(
np.array([
x for session_fmri_files in preproc_result['func']
for x in session_fmri_files
])[subject_fmri_perms[doc['subject']]])
break
# execute one GLM per subject
if do_preproc:
output_dir = out_dir
else:
output_dir = os.path.join(out_dir, "not_repreprocessed")
joblib.Parallel(n_jobs=max(n_jobs / 4, 1))(joblib.delayed(execute_glm)(
doc,
output_dir,
contrast_definitions,
outputs,
glm_model,
) for doc in docs)