def run_skullstrip(config, env):
fullext = config['outvol_fullext']
overwrite = config['overwrite']
refdir = config['refdir']
cmds = []
if not os.path.exists(refdir):
cmds.append('mkdir %(refdir)s' % config)
sumadir = config['sumadir']
sid = config['sid']
fs_sid = config['fs_sid']
if not sid:
raise ValueError("Subject id is not set, cannot continue")
# process the surfvol anatomical.
# because it's already skull stripped by freesurfer
# simply copy it over; rename brain.nii to surfvol_ss
surfvol_srcs = ['%s/%s' % (sumadir, fn) for fn in ['brain.nii', 'T1.nii']]
surfvol_trgs = [
'%s/%s' % (refdir, fn) for fn in
['%s_SurfVol_ss%s' % (sid, fullext),
'%s_SurfVol%s' % (sid, fullext)]
]
for src, trg in zip(surfvol_srcs, surfvol_trgs):
if os.path.exists(trg) and not overwrite:
print '%s already exists' % trg
else:
t_p, t_n, t_o, t_e = utils.afni_fileparts(trg)
trg_short = '%s%s' % (t_n, t_o)
cmds.append(
'cd "%s"; 3dresample -overwrite -orient LPI -inset %s -prefix ./%s'
% (refdir, src, trg_short))
cmds.append(
_set_vol_space_cmd('%s/%s+orig' % (refdir, t_n), config))
# process experimental volume.
expvol_src = config['expvol']
do_ss = config['expvol_ss']
[e_p, e_n, e_o, e_e] = utils.afni_fileparts(expvol_src)
expvol_trg_prefix = '%s%s' % (e_n, config['sssuffix'] if do_ss else '')
expvol_trg_tmp_prefix = '__tmp_%s' % expvol_trg_prefix
expvol_trg = '%s/%s%s' % (refdir, expvol_trg_prefix, fullext)
print "Attempt %s -> %s" % (expvol_src, expvol_trg)
ext = config['outvol_ext']
if overwrite or not utils.afni_fileexists(expvol_trg):
if do_ss:
cmds.append(
'cd "%s";3dSkullStrip -overwrite -prefix ./%s%s -input %s' %
(refdir, expvol_trg_tmp_prefix, ext, expvol_src))
else:
cmds.append('cd "%s";3dbucket -overwrite -prefix ./%s%s %s' %
(refdir, expvol_trg_tmp_prefix, ext, expvol_src))
cmds.append(
'cd "%s"; 3dresample -overwrite -orient LPI -prefix %s -inset %s%s'
% (refdir, expvol_trg_prefix, expvol_trg_tmp_prefix, ext))
cmds.append('rm %s/%s*' % (refdir, expvol_trg_tmp_prefix))
cmds.append(_set_vol_space_cmd(expvol_trg, config))
else:
print "No skull strip because already exists: %s%s" % (
expvol_trg_prefix, ext)
utils.run_cmds(cmds, env)
def run_skullstrip(config, env):
if config['identity']:
return
overwrite = config['overwrite']
refdir = config['refdir']
cmds = []
if not os.path.exists(refdir):
cmds.append('mkdir %(refdir)s' % config)
sumadir = config['sumadir']
sid = config['sid']
fs_sid = config['fs_sid']
if not sid:
raise ValueError("Subject id is not set, cannot continue")
# process the surfvol anatomical.
# because it's already skull stripped by freesurfer
# simply copy it over; rename brain.nii to surfvol_ss
surfvol_srcs = ['%s/%s' % (sumadir, fn) for fn in ['brain.nii', 'T1.nii']]
surfvol_trgs = [
'%s/%s' % (refdir, fn) for fn in
['%s_SurfVol_ss+orig.HEAD' %
sid, '%s_SurfVol+orig.HEAD' % sid]
]
for src, trg in zip(surfvol_srcs, surfvol_trgs):
if os.path.exists(trg) and not overwrite:
print '%s already exists' % trg
else:
t_p, t_n, t_o, t_e = utils.afni_fileparts(trg)
trg_short = '%s%s' % (t_n, t_o)
cmds.append('cd "%s"; 3dcopy -overwrite %s ./%s' %
(refdir, src, trg_short))
# process experimental volume.
expvol_src = config['expvol']
do_ss = config['expvol_ss']
[e_p, e_n, e_o, e_e] = utils.afni_fileparts(expvol_src)
expvol_trg_prefix = '%s%s' % (e_n, config['sssuffix'] if do_ss else '')
if 'nii' in e_e:
# ensure e_n+orig is in refdir
if overwrite or not utils.afni_fileexists('%s/%s+orig.HEAD' %
(refdir, e_n)):
print "Converting %s from NIFTI to AFNI format" % e_n
cmds.append('cd "%s"; 3dbucket -overwrite -prefix ./%s+orig %s' %
(refdir, e_n, expvol_src))
cmds.append(
'if [ -e %s/%s+tlrc.HEAD ]; then 3drefit -view orig -space ORIG %s/%s+tlrc; else echo "File in orig orientation - no refit necessary"; fi'
% (refdir, e_n, refdir, e_n))
expvol_src = '%s/%s+orig.HEAD' % (refdir, e_n)
expvol_trg = '%s/%s+orig.HEAD' % (refdir, expvol_trg_prefix)
print "Attempt %s -> %s" % (expvol_src, expvol_trg)
if overwrite or not utils.afni_fileexists(expvol_trg):
if do_ss:
cmds.append(
'cd "%s";3dSkullStrip -overwrite -prefix ./%s+orig -input %s' %
(refdir, expvol_trg_prefix, expvol_src))
else:
cmds.append('cd "%s";3dbucket -overwrite -prefix ./%s+orig %s' %
(refdir, expvol_trg_prefix, expvol_src))
else:
print "No skull strip because already exists: %s+orig" % expvol_trg_prefix
utils.run_cmds(cmds, env)
def run_skullstrip(config, env):
fullext = config['outvol_fullext']
overwrite = config['overwrite']
refdir = config['refdir']
cmds = []
if not os.path.exists(refdir):
cmds.append('mkdir %(refdir)s' % config)
sumadir = config['sumadir']
sid = config['sid']
fs_sid = config['fs_sid']
if not sid:
raise ValueError("Subject id is not set, cannot continue")
# process the surfvol anatomical.
# because it's already skull stripped by freesurfer
# simply copy it over; rename brain.nii to surfvol_ss
surfvol_srcs = ['%s/%s' % (sumadir, fn)
for fn in ['brain.nii',
'T1.nii']]
surfvol_trgs = ['%s/%s' % (refdir, fn)
for fn in ['%s_SurfVol_ss%s' % (sid, fullext),
'%s_SurfVol%s' % (sid, fullext)]]
for src, trg in zip(surfvol_srcs, surfvol_trgs):
if os.path.exists(trg) and not overwrite:
print '%s already exists' % trg
else:
t_p, t_n, t_o, t_e = utils.afni_fileparts(trg)
trg_short = '%s%s' % (t_n, t_o)
cmds.append('cd "%s"; 3dresample -overwrite -orient LPI -inset %s -prefix ./%s' %
(refdir, src, trg_short))
cmds.append(_set_vol_space_cmd('%s/%s+orig' % (refdir, t_n), config))
# process experimental volume.
expvol_src = config['expvol']
do_ss = config['expvol_ss']
[e_p, e_n, e_o, e_e] = utils.afni_fileparts(expvol_src)
expvol_trg_prefix = '%s%s' % (e_n, config['sssuffix'] if do_ss else '')
expvol_trg_tmp_prefix = '__tmp_%s' % expvol_trg_prefix
expvol_trg = '%s/%s%s' % (refdir, expvol_trg_prefix, fullext)
print "Attempt %s -> %s" % (expvol_src, expvol_trg)
ext = config['outvol_ext']
if overwrite or not utils.afni_fileexists(expvol_trg):
if do_ss:
cmds.append('cd "%s";3dSkullStrip -overwrite -prefix ./%s%s -input %s' %
(refdir, expvol_trg_tmp_prefix, ext, expvol_src))
else:
cmds.append('cd "%s";3dbucket -overwrite -prefix ./%s%s %s' %
(refdir, expvol_trg_tmp_prefix, ext, expvol_src))
cmds.append('cd "%s"; 3dresample -overwrite -orient LPI -prefix %s -inset %s%s' %
(refdir, expvol_trg_prefix, expvol_trg_tmp_prefix, ext))
cmds.append('rm %s/%s*' % (refdir, expvol_trg_tmp_prefix))
cmds.append(_set_vol_space_cmd(expvol_trg, config))
else:
print "No skull strip because already exists: %s%s" % (expvol_trg_prefix, ext)
utils.run_cmds(cmds, env)
def run_skullstrip(config, env):
if config['identity']:
return
overwrite = config['overwrite']
refdir = config['refdir']
cmds = []
if not os.path.exists(refdir):
cmds.append('mkdir %(refdir)s' % config)
sumadir = config['sumadir']
sid = config['sid']
fs_sid = config['fs_sid']
if not sid:
raise ValueError("Subject id is not set, cannot continue")
# process the surfvol anatomical.
# because it's already skull stripped by freesurfer
# simply copy it over; rename brain.nii to surfvol_ss
surfvol_srcs = ['%s/%s' % (sumadir, fn)
for fn in ['brain.nii',
'T1.nii']]
surfvol_trgs = ['%s/%s' % (refdir, fn)
for fn in ['%s_SurfVol_ss+orig.HEAD' % sid,
'%s_SurfVol+orig.HEAD' % sid]]
for src, trg in zip(surfvol_srcs, surfvol_trgs):
if os.path.exists(trg) and not overwrite:
print '%s already exists' % trg
else:
t_p, t_n, t_o, t_e = utils.afni_fileparts(trg)
trg_short = '%s%s' % (t_n, t_o)
cmds.append('cd "%s"; 3dcopy -overwrite %s ./%s' %
(refdir, src, trg_short))
# process experimental volume.
expvol_src = config['expvol']
do_ss = config['expvol_ss']
[e_p, e_n, e_o, e_e] = utils.afni_fileparts(expvol_src)
expvol_trg_prefix = '%s%s' % (e_n, config['sssuffix'] if do_ss else '')
if 'nii' in e_e:
# ensure e_n+orig is in refdir
if overwrite or not utils.afni_fileexists('%s/%s+orig.HEAD' % (refdir, e_n)):
print "Converting %s from NIFTI to AFNI format" % e_n
cmds.append('cd "%s"; 3dbucket -overwrite -prefix ./%s+orig %s' % (refdir, e_n, expvol_src))
cmds.append('if [ -e %s/%s+tlrc.HEAD ]; then 3drefit -view orig -space ORIG %s/%s+tlrc; else echo "File in orig orientation - no refit necessary"; fi' % (refdir, e_n, refdir, e_n))
expvol_src = '%s/%s+orig.HEAD' % (refdir, e_n)
expvol_trg = '%s/%s+orig.HEAD' % (refdir, expvol_trg_prefix)
print "Attempt %s -> %s" % (expvol_src, expvol_trg)
if overwrite or not utils.afni_fileexists(expvol_trg):
if do_ss:
cmds.append('cd "%s";3dSkullStrip -overwrite -prefix ./%s+orig -input %s' %
(refdir, expvol_trg_prefix, expvol_src))
else:
cmds.append('cd "%s";3dbucket -overwrite -prefix ./%s+orig %s' %
(refdir, expvol_trg_prefix, expvol_src))
else:
print "No skull strip because already exists: %s+orig" % expvol_trg_prefix
utils.run_cmds(cmds, env)
