def make_realignst(funcs, TR, logger):
"""use spm to reaign and slicetime correct files"""
stvars = utils.get_slicetime_vars(funcs, TR=TR)
meanfunc, realigned, params = utils.spm_realign(funcs)
if meanfunc is None:
logger.error('{0}: spm realignment failed'%(funcs))
return None, None
st_realigned = utils.spm_slicetime(realigned, stdict = stvars)
utils.zip_files(realigned[1:]) # first is original func
utils.zip_files([meanfunc])
if st_realigned is None:
logger.error('{0}: slice timing failed'.format(realigned))
return None, None
movement_array = np.loadtxt(params)
return st_realigned, movement_array
def process_subject(subdir, despike=False):
_, sid = os.path.split(subdir)
rawdir = os.path.join(subdir, "raw")
workdir = utils.defaults["realign_ants"]
if despike:
workdir = utils.defaults["despike"] + workdir
workdir, exists = utils.make_dir(subdir, workdir)
if exists:
raise IOError("{0}: skipping {1} exists".format(subdir, workdir))
funcs = split(rawdir, workdir, sid, despike)
aligned, move_arr = make_realign(funcs)
## Make aligned_4d
aligned4d = os.path.join(workdir, "align4d_{0}.nii.gz".format(sid))
aligned4d = utils.fsl_make4d(aligned, aligned4d)
print "aligned_4d:", aligned4d
plot_write_movement(workdir, sid, move_arr)
utils.zip_files(funcs)
utils.zip_files(aligned[1:])
print "{0} : finished".format(sid)
def process_subject(subdir, tr, logger, despike=False):
""" process one subject despike (optional), realign and
do slicetime correction via SPM tools"""
globstr = 'B*func4d.nii*'
workdirnme = utils.defaults['realign_spm']
if despike:
workdirnme = utils.defaults['despike'] + workdirnme
globstr = 'ds' + globstr
_, sid = os.path.split(subdir)
rawdir = os.path.join(subdir, 'raw')
workdir, exists = utils.make_dir(subdir, workdirnme)
if exists:
logger.error('{0}: skipping {1} exists'.format(subdir, workdir))
return None
funcs = split(rawdir, workdir, sid, logger, globstr)
if funcs is None:
logger.error('Raw dir missing data: {0}'.format(rawdir))
return None
staligned, move_arr = make_realignst(funcs, tr, logger)
if staligned is None:
return None
## Make aligned_4d
aligned4d = os.path.join(workdir, 'align4d_{0}.nii.gz'.format(sid))
aligned4d = utils.fsl_make4d(staligned, aligned4d)
logger.info(aligned4d)
## spm only has 6 params, add empty 7th for plotting
move_arr = np.hstack((move_arr,
np.zeros((move_arr.shape[0],1))))
plot_write_movement(workdir, sid, move_arr, logger)
## zip files
utils.zip_files(funcs)
utils.zip_files(staligned)
logger.info('{0} : finished'.format(sid))
