def applywarp(lst_b0, lst_fn):
lst_fnout = []
for i in range(len(lst_b0)):
mat = '%s_to_mean.mat0GenericAffine.mat' % lst_b0[i]
f_in = lst_fn[i]
f_out = filename_wo_ext(os.path.basename(lst_fn[i])) + '_rigid.nii.gz'
cmd = 'antsApplyTransforms -d 3 -e 3 -i %s -r %s.nii.gz -o %s -n BSpline[3] -t %s' \
% (f_in, lst_b0[i], f_out, mat)
run_command(cmd)
lst_fnout.append(f_out)
return lst_fnout
def xalign(lst_b0, t):
for i in range(len(lst_b0)):
mat = '%s_to_mean.mat' % lst_b0[i]
cmd = 'antsRegistration -d 3 \
-n BSpline[3] \
--convergence 10 \
--transform Rigid[3] \
--smoothing-sigmas 0mm \
--metric MI[%s.nii.gz,%s_xenc.nii.gz,1,16] \
-o [%s,%s_xenc.nii.gz] \
--masks [%s,%s] \
--shrink-factors 1 \
' % (bn_mean, lst_b0[i], fn_tempmat, lst_b0[i], fn_mask,
fn_mask)
run_command(cmd)
if t == 0:
run_command('cp %s0GenericAffine.mat %s0GenericAffine.mat' %
(fn_tempmat, mat))
else:
cmd = 'ComposeMultiTransform 3 %s0GenericAffine.mat %s0GenericAffine.mat %s0GenericAffine.mat' \
% (mat, fn_tempmat, mat)
#% (mat, mat, fn_tempmat)
run_command(cmd)
def init(lst_b0):
for i in range(len(lst_b0)):
mat = '%s_to_mean.mat' % lst_b0[i]
#run_command('cp %s %s' % (identmat, mat))
run_command('cp %s.nii.gz %s_xenc.nii.gz' % (lst_b0[i], lst_b0[i]))
def calc(lst_b0):
run_command('fslmerge -t %s_concat %s' %
(bn_mean, ' '.join(['%s_xenc' % tmp for tmp in (lst_b0)])))
run_command('fslmaths %s_concat -Tmean %s' % (bn_mean, bn_mean))
filename).split('/')[-1].split('_')[0], middle,
os.path.basename(filename))
else:
lst_dwi[i] = '%sordered%s_%s_%s' % (prefix, i + 1, middle,
os.path.basename(filename))
lst_b0 = []
lst_fn = []
lst_nframe = []
for i in range(len(lst_dwi)):
fn_dwi = os.path.join(dn_base, lst_dwi[i])
lst_fn.append(fn_dwi)
lst_nframe.append(nib.load(fn_dwi).shape[-1])
fn_dwi_wo_ext = filename_wo_ext(fn_dwi)
bn_dwi = os.path.basename(fn_dwi_wo_ext)
run_command('extract_b0_dwi_mean.py %s %s.bval %s' %
(fn_dwi, fn_dwi_wo_ext, os.path.basename(fn_dwi)))
lst_b0.append('%s_b0' % bn_dwi)
if False:
subject = lst_b0[0].split('_')
is_number = False
for i in range(len(subject)):
try:
int(subject[i])
except:
pass
else:
is_number = True
if is_number:
break
subject = '_'.join(subject[:i])