def _set_vol_space_cmd(fn, config):
param = ''
del_cmd = ''
p, n, o, e = utils.afni_fileparts(fn)
space = config.get('outvol_space', None)
if space is not None:
param += ' -space %s' % space
view = config.get('outvol_view')
if view is not None:
param += ' -view %s' % view
if len(o) and o[0] == '+' and o[1:].lower() != view.lower():
trgfn = '%s/%s+%s' % (p, n, view.lower())
del_cmd = 'rm %s*; ' % trgfn
if param:
p, n, o, e = utils.afni_fileparts(fn)
cmd = 'cd %s; %s 3drefit -overwrite %s %s' % (p, del_cmd, param, n + o + e)
else:
cmd = 'echo "Not changing view or space for %s"' % fn
return cmd
def _ext(config, for1D=False):
'''Returns the extension for a file name'''
if _is_surf(config):
return '.1D.dset' if for1D else '.niml.dset'
else:
fn = config['data_files'][0]
return ''.join(utils.afni_fileparts(fn)[2:])
def _convert_vol_space_to_orig_cmd(fn):
p, n, o, e = utils.afni_fileparts(fn)
if o == '+orig':
return "echo '%s' is already in orig space - no conversion" % fn
t = '__tmp_foo_'
while os.path.exists(p + '/' + t + o + e):
t += 'x'
cmds = ['cd %s' % p,
'3drename -overwrite %s%s %s%s' % (n, o, t, o),
'3drefit -view orig %s%s' % (t, o),
'3drename -overwrite %s+orig %s+orig' % (t, n)]
return ';'.join(cmds)
def _remove_files(config, list_of_files):
# removes a list of files, if config allows for it
# in the case of AFNI volume files, it removes HEAD and BRIK files
if not config['keep_files']:
for fn in list_of_files:
fp = utils.afni_fileparts(fn)
if fp[2]:
# AFNI HEAD/BRIK combination
# ensure we delete all of them
exts = ['.HEAD', '.BRIK', '.BRIK.gz']
fn = ''.join(fp[1:3])
else:
exts = ['']
for ext in exts:
full_fn = os.path.join(config['output_dir'], fn + ext)
if os.path.exists(full_fn):
os.remove(full_fn)
def run_makesurfmasks(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
if config['sid'] is None:
raise ValueError('Need sid')
sumfn = '%s_qa_surf_mask' % config['sid'] # output file
fullext = config['outvol_fullext']
volor = config['outvol_ext']
sumfn_path = '%s/%s%s' % (refdir, sumfn, fullext)
qafn_path = '%s/%s.png' % (refdir, sumfn)
checkfn_paths = (sumfn_path, qafn_path)
if all(map(os.path.exists, checkfn_paths)) and not overwrite:
print "Already exist: %s" % (", ".join(checkfn_paths))
return
icolds, hemis = _get_hemis_icolds(config)
volexts = ['%s%s' % (volor, e) for e in '.HEAD', '.BRIK*']
sssuffix = config['sssuffix'] if config['expvol_ss'] else ''
expvol_fn = '%s%s%s' % (utils.afni_fileparts(config['expvol'])[1],
sssuffix,
volor)
#if overwrite or not os.path.exists('%s/%s' % (refdir, sv_al_nii_fn)):
# cmd = 'cd %s; 3dcopy -overwrite %s %s' % (refdir, sv_al_orig_fn, sv_al_nii_fn)
# utils.run_cmds(cmd, env)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
icold = max(icolds)
oneDfn = '__t.1D'
oneDtfn = '__tt.1D' # transposed
cmds = ['cd %s' % refdir,
'1deval -1D: -num %d -expr 1 > %s' % (icold ** 2 * 10 + 1, oneDfn),
'1dtranspose %s > %s' % (oneDfn, oneDtfn)]
utils.run_cmds(';'.join(cmds), env)
tmpfns = [oneDfn, oneDtfn]
s2v_cmd = ('3dSurf2Vol -map_func mask2 -data_expr "a*%%d" -spec %%s %%s -sv %s'
' -grid_parent %s. -prefix %%s -sdata %s -overwrite') % \
(expvol_fn, expvol_fn, oneDtfn)
infix2val = {'-surf_A pial':1,
'-surf_A smoothwm':2,
'-surf_A smoothwm -surf_B pial -f_steps 20': 4}
volfns = []
for hemi in hemis:
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
for infix, val in infix2val.iteritems():
fnprefix = '__m%d_%sh' % (val, hemi)
cmd = s2v_cmd % (val, specfn, infix, fnprefix)
utils.run_cmds('cd %s;%s' % (refdir, cmd))
tmpfns.extend(['%s%s' % (fnprefix, e) for e in volexts])
volfns.append(fnprefix + volor)
cmds = ['cd %s' % refdir]
catfn = '__cat'
cmds.extend(['3dTcat -overwrite -prefix %s %s' % (catfn, ' '.join(volfns)),
'3dTstat -overwrite -sum -prefix %s %s%s' % (sumfn, catfn, volor)])
tmpfns.extend(['%s%s' % (catfn, e) for e in volexts])
cmds.extend('rm %s' % fn for fn in tmpfns)
cmds.append('echo "Surface mask in %s"' % sumfn)
utils.run_cmds(';'.join(cmds), env)
# make plot
if overwrite or not os.path.exists(qafn_path):
expvol_path = '%s/%s' % (refdir, expvol_fn)
_make_slice_plot(expvol_path,
sumfn_path,
qafn_path)
def run_alignment(config, env):
'''Aligns anat (which is assumed to be aligned with EPI data) to FreeSurfer SurfVol
This function strips the anatomicals (by default), then uses align_epi_anat.py
to estimate the alignment, then applies this transformation to the non-skull-stripped
SurfVol and also to the surfaces. Some alignment headers will be nuked'''
overwrite = config['overwrite']
alignsuffix = config['al2expsuffix']
refdir = config['refdir']
fullext = config['outvol_fullext']
ext = config['outvol_ext']
if config['sid'] is None:
raise ValueError('Need sid')
cmds = []
if not os.path.exists(config['refdir']):
cmds.append('mkdir %(refdir)s' % config)
# two volumes may have to be stripped: the inpput anatomical, and the surfvol.
# put them in a list here and process them similarly
surfvol = '%(refdir)s/%(sid)s_SurfVol%(outvol_fullext)s' % config
surfvol_ss = '%(refdir)s/%(sid)s_SurfVol%(sssuffix)s%(outvol_fullext)s' % config
e_p, e_n, _, _ = utils.afni_fileparts(config['expvol'])
if config['expvol_ss']:
e_n = '%s%s' % (e_n, config['sssuffix'])
expvol = '%s/%s%s' % (refdir, e_n, fullext)
volsin = [surfvol_ss, expvol]
for volin in volsin:
if not os.path.exists(volin):
raise ValueError('File %s does not exist' % volin)
a_n = utils.afni_fileparts(volsin[0])[1] # surfvol input root name
ssalprefix = '%s%s' % (a_n, alignsuffix)
unity = "1 0 0 0 0 1 0 0 0 0 1 0" # we all like unity, don't we?
fullmatrixfn = '%s_mat.aff12.1D' % ssalprefix
aloutfns = ['%s%s' % (ssalprefix, fullext), fullmatrixfn] # expected output files if alignment worked
if config['overwrite'] or not all([os.path.exists('%s/%s' % (refdir, f)) for f in aloutfns]):
alignedfn = '%s/%s%s' % (refdir, ssalprefix, fullext)
if config['identity']:
fullmatrix_content = '"MATRIX(%s)"' % unity.replace(" ", ",")
cmd = 'cd "%s"; cat_matvec %s > %s; 3dcopy -overwrite %s%s %s%s%s' % (refdir, fullmatrix_content, fullmatrixfn, a_n, ext, a_n, alignsuffix, ext)
else:
# use different inputs depending on whether expvol is EPI or ANAT
twovolpat = ('-anat %s -epi %s -anat2epi -epi_base 0 -anat_has_skull no -epi_strip None' if config['isepi']
else '-dset1 %s -dset2 %s -dset1to2 -dset1_strip None -dset2_strip None')
# use this pattern to generate a suffix
twovolsuffix = twovolpat % (volsin[0], volsin[1])
aea_opts = config['aea_opts']
if config['template']:
aea_opts += " -Allineate_opts '-maxrot 10 -maxshf 10 -maxscl 1.5'"
# align_epi_anat.py
cmd = 'cd "%s"; align_epi_anat.py -overwrite -suffix %s %s %s' % (refdir, alignsuffix, twovolsuffix, aea_opts)
cmds.append(cmd)
cmds.append(_set_vol_space_cmd(alignedfn, config))
utils.run_cmds(cmds, env)
else:
print "Alignment already done - skipping"
# run these commands first, then check if everything worked properly
cmds = []
# see if the expected transformation file was found
if not config['identity'] and not os.path.exists('%s/%s' % (refdir, fullmatrixfn)):
raise Exception("Could not find %s in %s" % (fullmatrixfn, refdir))
# now make a 3x4 matrix
matrixfn = '%s%s.A2E.1D' % (a_n, alignsuffix)
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn)):
cmds.append('cd "%s"; cat_matvec %s > %s || exit 1' % (refdir, fullmatrixfn, matrixfn))
# make an aligned, non-skullstripped version of SurfVol in refdir
alprefix = '%s_SurfVol%s' % (config['sid'], alignsuffix)
svalignedfn = '%s/%s%s' % (refdir, alprefix, fullext)
newgrid = 1 # size of anatomical grid in mm. We'll have to resample, otherwise 3dWarp does
# not respect the corners of the volume (as of April 2012)
if overwrite or not os.path.exists(svalignedfn):
#if not config['fs_sid']:
# raise ValueError("Don't have a freesurfer subject id - cannot continue")
#surfvolfn = '%s/%s_SurfVol+orig' % (config['sumadir'], config['fs_sid'])
surfvolfn = '%s/T1.nii' % config['sumadir']
cmds.append('cd "%s";3dWarp -overwrite -newgrid %f -matvec_out2in `cat_matvec -MATRIX %s` -prefix ./%s %s' %
(refdir, newgrid, matrixfn, alprefix, surfvolfn))
cmds.append(_set_vol_space_cmd('%s/%s+orig' % (refdir, alprefix), config))
else:
print '%s already exists - skipping Warp' % svalignedfn
utils.run_cmds(cmds, env)
cmds = []
# nuke afni headers
headernukefns = ['%s%s' % (f, fullext) for f in [ssalprefix, alprefix]]
headernukefields = ['ALLINEATE_MATVEC_B2S_000000',
'ALLINEATE_MATVEC_S2B_000000',
'WARPDRIVE_MATVEC_FOR_000000',
'WARPDRIVE_MATVEC_INV_000000']
for fn in headernukefns:
for field in headernukefields:
# nuke transformation - otherwise AFNI does this unwanted transformation for us
fullfn = '%s/%s' % (refdir, fn)
if not (os.path.exists(fullfn) or config['identity']):
raise ValueError("File %r does not exist" % fullfn)
refitcmd = "3drefit -atrfloat %s '%s' %s" % (field, unity, fn)
# only refit if not already in AFNI history (which is stored in HEADfile)
cmd = 'cd "%s"; m=`grep "%s" %s | wc -w`; if [ $m -eq 0 ]; then %s; else echo "File %s seems already 3drefitted"; fi' % (refdir, refitcmd, fn, refitcmd, fn)
cmds.append(cmd)
utils.run_cmds('; '.join(cmds), env)
cmds = []
# run AddEdge so that volumes can be inspected visually for alignment
if config['AddEdge']:
use_ss = config['expvol_ss']
# ae_{e,s}_n are AddEdge names for expvol and surfvol
ae_e_n = utils.afni_fileparts(config['expvol'])[1]
if use_ss:
ae_e_n += config['sssuffix']
ae_s_n = ssalprefix #if use_ss else alprefix
# *_ne have the output extension as well
ae_e_ne = ae_e_n + ext
ae_s_ne = ae_s_n + ext
addedge_fns = ['%s/_ae.ExamineList.log' % refdir]
exts = ['HEAD', 'BRIK']
orig_ext = '+orig'
addedge_rootfns = ['%s_%s%%s' % (ae_e_n, postfix)
for postfix in ['e3', 'ec', ae_s_n + '_ec']]
addedge_rootfns.extend(['%s_%s%%s' % (ae_s_n, postfix)
for postfix in ['e3', 'ec']])
addedge_fns_pat = ['%s.%s' % (fn, e) for fn in addedge_rootfns for e in exts]
addegde_pathfns_orig = map(lambda x:os.path.join(refdir, x % '+orig'), addedge_fns_pat) + addedge_fns
addegde_pathfns_ext = map(lambda x:os.path.join(refdir, x % ext), addedge_fns_pat)
addegde_exists = map(os.path.exists, addegde_pathfns_ext)
if overwrite or not all(addegde_exists):
ae_ns = (ae_e_n, ae_s_n)
cmds.extend(map(lambda fn : 'if [ -e "%s" ]; then rm "%s"; fi' % (fn, fn), addegde_pathfns_orig + addegde_pathfns_ext))
cmds.append(';'.join(['cd %s' % refdir] +
[_convert_vol_space_to_orig_cmd('%s/%s%s' % (refdir, n, ext))
for n in ae_ns] +
['\@AddEdge %s+orig %s+orig' % ae_ns]))
set_space_fns = addegde_pathfns_orig + ['%s/%s%s.%s' % (refdir, fn, orig_ext, exts[0]) for fn in ae_ns]
for fn in set_space_fns: #['%s/%s' % (refdir, fn % orig_ext) for fn in addedge_fns_pat]:
if fn.endswith('.log'):
continue
cmds.append('if [ -e %s ]; then %s; fi' % (fn, _set_vol_space_cmd(fn, config)))
utils.run_cmds(cmds, env)
cmds = []
else:
print "AddEdge seems to have been run already"
sid = config['sid']
plot_slice_fns = [(ae_e_n + '_e3', ae_s_n + '_e3', '%s_qa_e3.png' % sid),
(None, ae_e_n + '_' + ae_s_n + '_ec', '%s_qa_ec.png' % sid)]
plot_slice_imgfns = ['%s/%s' % (refdir, fn) for fn in plot_slice_fns]
if overwrite or not all(map(os.path.exists, plot_slice_imgfns)):
slice_dims = [0, 1, 2]
slice_pos = [.35, .45, .55, .65]
for fns in plot_slice_fns:
input_fns = []
for i, fn in enumerate(fns):
if fn is not None:
fn = '%s/%s' % (refdir, fn)
if i <= 1:
fn += ext
input_fns.append(fn)
fn1, fn2, fnout = input_fns
if not os.path.exists(fnout):
_make_slice_plot(fn1, fn2, fnout)
print "QA Image saved to %s" % fnout
else:
print "Already exists: %s" % fnout
else:
print "QA images already exist"
# because AFNI uses RAI orientation but FreeSurfer LPI, make a new
# affine transformation matrix in which the signs of
# x and y coordinates are negated before and after the transformation
matrixfn_LPI2RAI = '%s.A2E_LPI.1D' % ssalprefix
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn_LPI2RAI)):
lpirai = '"MATRIX(-1,0,0,0,0,-1,0,0,0,0,1,0)"'
cmd = ('cd %s; cat_matvec -ONELINE %s `cat_matvec -MATRIX %s` %s > %s' %
(refdir, lpirai, matrixfn, lpirai, matrixfn_LPI2RAI))
cmds.append(cmd)
# apply transformation to surfaces
[icolds, hemis] = _get_hemis_icolds(config)
sumadir = config['sumadir']
sumafiles = os.listdir(sumadir)
origext = '.asc'
ext = format2extension(config)
tp = format2type(config)
# process all hemispheres and ld values
for icold in icolds:
for hemi in hemis:
pat = '%s%sh.?*%s' % (config['mi_icopat'] % icold, hemi, origext)
for sumafile in sumafiles:
if fnmatch.fnmatch(sumafile, pat):
if not sumafile.endswith(origext):
raise ValueError("%s does not end with %s" % (sumafile, origext))
#s = sumafile.split(".")
#s[len(s) - 2] += config['alsuffix'] # insert '_al' just before last dot
#alsumafile = ".".join(s)
extsumafile = sumafile[:-len(origext)]
alsumafile = extsumafile + config['alsuffix'] + ext
if config['overwrite'] or not os.path.exists('%s/%s' % (refdir, alsumafile)):
# now apply transformation
cmd = 'cd "%s";ConvertSurface -overwrite -i_fs %s/%s -o_%s ./%s -ixmat_1D %s' % \
(refdir, sumadir, sumafile, tp, alsumafile, matrixfn_LPI2RAI)
cmds.append(cmd)
# as of June 2012 copy the original sphere.reg (not aligned) as well
if sumafile == ('%s.sphere.reg%s' % (pat, ext)):
sumaout = '%s/%s' % (refdir, extsumafile + ext)
if config['overwrite'] or not os.path.exists(sumaout):
s = surf.read('%s/%s' % (sumadir, sumafile))
surf.write(s, sumaout)
#cmds.append('cp %s/%s %s/%s' % (sumadir, sumafile, refdir, sumafile))
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
srcpathfn = os.path.join(sumadir, mapfn)
if os.path.exists(srcpathfn):
trgpathfn = os.path.join(refdir, mapfn)
if not os.path.exists(trgpathfn) or config['overwrite']:
cmds.append('cp %s %s' % (srcpathfn, trgpathfn))
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 augmentconfig(c):
'''add more configuration values that are *derived* from the current configuration,
and also checks whether some options are set properly'''
# ensure surfdir is set properly.
# normally it should end in 'surf'
# try to be smart and deduce subject id from surfdir (if not set explicitly)
surfdir = c['surfdir']
if surfdir:
surfdir = os.path.abspath(surfdir)
parent, nm = os.path.split(surfdir)
if nm != 'surf':
jn = os.path.join(surfdir, 'surf')
if os.path.exists(jn):
surfdir = jn
elif nm == 'SUMA':
surfdir = parent
if not (os.path.exists(surfdir) or os.path.split(surfdir)[1] == 'surf'):
print('Warning: surface directory %s not does exist or does not end in "surf"' % surfdir)
surfdir = None
c['surfdir'] = surfdir
# set SUMADIR as well
c['sumadir'] = '%(surfdir)s/SUMA/' % c
# derive subject id from surfdir
sid = os.path.split(os.path.split(surfdir)[0])[1] if surfdir else None
if c.get('sid') is None:
c['sid'] = sid
if c['sid'] is None:
print"Warning: no subject id specified"
c['prefix_sv2anat'] = 'SurfVol2anat'
# update steps
if c.get('steps', 'all') == 'all':
c['steps'] = 'toafni+mapico+moresurfs+skullstrip+align+makespec+makespecboth+makesurfmasks'
hasanatvol = 'anatvol' in c and c['anatvol']
hasepivol = 'epivol' in c and c['epivol']
hasexpvol = 'expvol' in c and c['expvol']
hasisepi = 'isepi' in c
if hasexpvol:
if hasanatvol or hasepivol:
raise Exception("expvol specified, but also anatvol or epivol - illegal!")
if not hasisepi:
raise Exception("not specified whether expvol is EPI (yes) or anat (no)")
else:
if hasanatvol:
if 'epivol' in c and c['epivol']:
raise Exception("Cannot have both anatvol and epivol")
else:
c['expvol'] = c['anatvol']
c['isepi'] = False
del(c['anatvol'])
else:
if hasepivol:
c['expvol'] = c['epivol']
c['isepi'] = True
del(c['epivol'])
else:
print("Warning: no anatomical or functional experimental voume defined")
def yesno2bool(d, k): # dict, key
'''Assuming d[k] contains the word 'yes' or 'no', makes d[k] a boolean
(True=='yes',False=='no'); otherwise an exception is thrown. The dict is updated'''
val = d[k]
if val is None:
b = False
elif type(val) == bool:
b = val
else:
v = val.lower()
if v == 'yes':
b = True
elif v == 'no':
b = False
else:
raise Exception("Not yes or no: %s" % val)
d[k] = b
yesno2bool(c, 'AddEdge')
if c['identity']:
c['expvol_ss'] = c['anatval_ss'] = False
else:
yesno2bool(c, 'expvol_ss')
yesno2bool(c, 'isepi')
# see if we can get the fs_sid
# (only if surfdir is set properly)
# XXX not sure if this still makes sense
c['fs_sid'] = None
surfdir = c.get('surfdir', None)
if not surfdir is None and os.path.exists(surfdir):
fs_log_fn = os.path.join(surfdir, '..', 'scripts', 'recon-all.done')
print "Looking in %s" % fs_log_fn
if os.path.exists(fs_log_fn):
with open(fs_log_fn) as f:
lines = f.read().split('\n')
for line in lines:
if line.startswith('SUBJECT'):
fs_sid = line[8:]
c['fs_sid'] = fs_sid
print "Found Freesurfer sid %s" % fs_sid
break
if c['fs_sid'] is None:
c['fs_sid'] = sid
print "Unable to find proper Freesurfer sid"
pathvars = ['anatvol', 'expvol', 'epivol', 'refdir', 'surfdir']
for pathvar in pathvars:
if pathvar in c and c[pathvar]:
c[pathvar] = os.path.abspath(c[pathvar])
print "Set absolute path for %s: %s" % (pathvar, c[pathvar])
if c['template'] and c['notemplate']:
error('Cannot have both template and notemplate')
if 'expvol' in c:
p, n, o, e = utils.afni_fileparts(c['expvol'])
if c.get('outvol_space', None) is None:
cmd = '3dAttribute TEMPLATE_SPACE %s' % c['expvol']
outvol_space = utils.cmd_capture_output(cmd)
outvol_space = outvol_space.split('~')[0].strip()
if len(outvol_space) and not c['notemplate'] and outvol_space.lower() != 'orig':
print "Detected TEMPLATE_SPACE=%s" % outvol_space
c['outvol_space'] = outvol_space
if o == '+orig':
o = '+tlrc'
print "Template space '%s' detected: output has extension %s" % (outvol_space, o)
c['template'] = True
else:
c['outvol_space'] = '+orig'
if len(o): #'+orig' or '+tlrc'
c['outvol_ext'] = o
c['outvol_fullext'] = o + e
c['outvol_view'] = o[1:]
else:
# For NIFTI - output in orig or tlrc
c['outvol_view'] = 'tlrc' if c['template'] else 'orig'
c['outvol_ext'] = '+' + c['outvol_view']
c['outvol_fullext'] = c['outvol_ext'] + '.HEAD'
return c
