def task_fetch_data():
"""Step 00: Download the openfmri ds117 dataset files."""
for subject in subjects:
t1_fname = fname.t1(subject=subject)
sss_fnames = [fname.sss(subject=subject, run=run) for run in range(1, 7)]
flash5_fname = fname.flash5(subject=subject)
yield dict(
name=subject,
file_dep=['00_fetch_data.py'],
targets=[t1_fname, flash5_fname] + sss_fnames,
actions=['python 00_fetch_data.py %s' % subject],
)
def task_anatomy():
"""Step 01: Run the FreeSurfer anatomical-MRI segmentation program."""
for subject in subjects:
t1_fname = fname.t1(subject=subject)
surf_fnames = [fname.surface(subject=subject, surf=surf)
for surf in ['inner_skull', 'outer_skull', 'outer_skin']]
bem_fname = fname.bem(subject=subject)
yield dict(
name=subject,
task_dep=['fetch_data'],
file_dep=[t1_fname, '01_anatomy.py'],
targets=surf_fnames + [bem_fname],
actions=['python 01_anatomy.py %s' % subject],
)
def tee_output(command, log_file):
"""Write the output of a command to a logfile as well as stdout."""
print('Writing the output of the command below to', log_file)
print(' '.join(command))
with open(log_file, 'wb') as fid:
proc = subprocess.Popen(
command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
for line in proc.stdout:
fid.write(line)
if proc.wait() != 0:
raise RuntimeError('Command failed')
tee_output(['recon-all', '-all', '-s', subject, '-sd', fname.subjects_dir,
'-i', fname.t1(subject=subject)],
fname.freesurfer_log(subject=subject))
print('Copying FLASH files')
os.makedirs(fname.flash_dir(subject=subject), exist_ok=True)
for f_src in glob.glob(fname.flash_glob(subject=subject)):
f_dst = op.basename(f_src).replace("meflash_", "mef")
f_dst = op.join(fname.flash_dir(subject=subject), f_dst)
shutil.copy(f_src, f_dst)
# Fix the headers for subject 19
if subject == 'sub019':
print('Fixing FLASH files for %s' % (subject,))
flash_files = (['mef05_%d.mgz' % x for x in range(7)] +
['mef30_%d.mgz' % x for x in range(7)])
"""Write the output of a command to a logfile as well as stdout."""
print('Writing the output of the command below to', log_file)
print(' '.join(command))
with open(log_file, 'wb') as fid:
proc = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
for line in proc.stdout:
fid.write(line)
if proc.wait() != 0:
raise RuntimeError('Command failed')
tee_output([
'recon-all', '-all', '-s', subject, '-sd', fname.subjects_dir, '-i',
fname.t1(subject=subject)
], fname.freesurfer_log(subject=subject))
print('Copying FLASH files')
os.makedirs(fname.flash_dir(subject=subject), exist_ok=True)
for f_src in glob.glob(fname.flash_glob(subject=subject)):
f_dst = op.basename(f_src).replace("meflash_", "mef")
f_dst = op.join(fname.flash_dir(subject=subject), f_dst)
shutil.copy(f_src, f_dst)
# Fix the headers for subject 19
if subject == 'sub019':
print('Fixing FLASH files for %s' % (subject, ))
flash_files = (['mef05_%d.mgz' % x for x in range(7)] +
['mef30_%d.mgz' % x for x in range(7)])