param_file = fname_presuffix(anat_file.replace('_corrected', ''),
newpath=sammba_params_dir,
suffix='_bil2_transform.1D',
use_ext=False)
sammba_anat_file = fname_presuffix(anat_file,
newpath=sammba_transformed_dir,
prefix='bil2_transfo_')
sammba_atlas_file = fname_presuffix(atlas_file,
newpath=sammba_transformed_dir,
prefix='bil2_transfo_')
print(anat_file)
assert (os.path.isfile(raw_atlas_file))
allineate = afni.Allineate().run
copy_geom = fsl.CopyGeom().run
if True:
out_allineate = allineate(in_file=anat_file,
master=anat_file,
in_param_file=param_file,
nwarp='bilinear',
out_file=sammba_anat_file,
environ={'AFNI_DECONFLICT': 'OVERWRITE'})
out_copy_geom = copy_geom(dest_file=sammba_anat_file,
in_file=anat_file)
out_allineate = allineate(in_file=raw_atlas_file,
master=raw_atlas_file,
in_param_file=param_file,
nwarp='bilinear',
final_interpolation='nearestneighbour',
def coregister_fmri_session(session_data,
t_r,
write_dir,
brain_volume,
use_rats_tool=True,
slice_timing=True,
prior_rigid_body_registration=False,
caching=False,
voxel_size_x=.1,
voxel_size_y=.1,
verbose=True,
**environ_kwargs):
"""
Coregistration of the subject's functional and anatomical images.
The functional volume is aligned to the anatomical, first with a rigid body
registration and then on a per-slice basis (only a fine correction, this is
mostly for correction of EPI distortion).
Parameters
----------
session_data : sammba.registration.SessionData
Single animal data, giving paths to its functional and anatomical
image, as well as it identifier.
t_r : float
Repetition time for the EPI, in seconds.
write_dir : str
Directory to save the output and temporary images.
brain_volume : int
Volume of the brain in mm3 used for brain extraction.
Typically 400 for mouse and 1800 for rat.
use_rats_tool : bool, optional
If True, brain mask is computed using RATS Mathematical Morphology.
Otherwise, a histogram-based brain segmentation is used.
prior_rigid_body_registration : bool, optional
If True, a rigid-body registration of the anat to the func is performed
prior to the warp. Useful if the images headers have missing/wrong
information.
voxel_size_x : float, optional
Resampling resolution for the x-axis, in mm.
voxel_size_y : float, optional
Resampling resolution for the y-axis, in mm.
caching : bool, optional
Wether or not to use caching.
verbose : bool, optional
If True, all steps are verbose. Note that caching implies some
verbosity in any case.
environ_kwargs : extra arguments keywords
Extra arguments keywords, passed to interfaces environ variable.
Returns
-------
the same sequence with each animal_data updated: the following attributes
are added
- `output_dir_` : str
Path to the output directory.
- `coreg_func_` : str
Path to paths to the coregistered functional image.
- `coreg_anat_` : str
Path to paths to the coregistered functional image.
- `coreg_transform_` : str
Path to the transform from anat to func.
Notes
-----
If `use_rats_tool` is turned on, RATS tool is used for brain extraction
and has to be cited. For more information, see
`RATS <http://www.iibi.uiowa.edu/content/rats-overview/>`_
"""
func_filename = session_data.func
anat_filename = session_data.anat
environ = {'AFNI_DECONFLICT': 'OVERWRITE'}
for (key, value) in environ_kwargs.items():
environ[key] = value
if verbose:
terminal_output = 'allatonce'
else:
terminal_output = 'none'
if use_rats_tool:
if segmentation.interfaces.Info().version() is None:
raise ValueError('Can not locate RATS')
else:
ComputeMask = segmentation.MathMorphoMask
else:
ComputeMask = segmentation.HistogramMask
if ants.base.Info().version is None:
raise ValueError('Can not locate ANTS')
if caching:
memory = Memory(write_dir)
tshift = memory.cache(afni.TShift)
clip_level = memory.cache(afni.ClipLevel)
volreg = memory.cache(afni.Volreg)
allineate = memory.cache(afni.Allineate)
tstat = memory.cache(afni.TStat)
compute_mask = memory.cache(ComputeMask)
calc = memory.cache(afni.Calc)
allineate = memory.cache(afni.Allineate)
allineate2 = memory.cache(afni.Allineate)
unifize = memory.cache(afni.Unifize)
bias_correct = memory.cache(ants.N4BiasFieldCorrection)
catmatvec = memory.cache(afni.CatMatvec)
warp = memory.cache(afni.Warp)
resample = memory.cache(afni.Resample)
slicer = memory.cache(afni.ZCutUp)
warp_apply = memory.cache(afni.NwarpApply)
qwarp = memory.cache(afni.Qwarp)
merge = memory.cache(afni.Zcat)
copy_geom = memory.cache(fsl.CopyGeom)
overwrite = False
for step in [
tshift, volreg, allineate, allineate2, tstat, compute_mask,
calc, unifize, resample, slicer, warp_apply, qwarp, merge
]:
step.interface().set_default_terminal_output(terminal_output)
else:
tshift = afni.TShift(terminal_output=terminal_output).run
clip_level = afni.ClipLevel().run
volreg = afni.Volreg(terminal_output=terminal_output).run
allineate = afni.Allineate(terminal_output=terminal_output).run
allineate2 = afni.Allineate(terminal_output=terminal_output
).run # TODO: remove after fixed bug
tstat = afni.TStat(terminal_output=terminal_output).run
compute_mask = ComputeMask(terminal_output=terminal_output).run
calc = afni.Calc(terminal_output=terminal_output).run
unifize = afni.Unifize(terminal_output=terminal_output).run
bias_correct = ants.N4BiasFieldCorrection(
terminal_output=terminal_output).run
catmatvec = afni.CatMatvec().run
warp = afni.Warp().run
resample = afni.Resample(terminal_output=terminal_output).run
slicer = afni.ZCutUp(terminal_output=terminal_output).run
warp_apply = afni.NwarpApply(terminal_output=terminal_output).run
qwarp = afni.Qwarp(terminal_output=terminal_output).run
merge = afni.Zcat(terminal_output=terminal_output).run
copy_geom = fsl.CopyGeom(terminal_output=terminal_output).run
overwrite = True
session_data._check_inputs()
output_dir = os.path.join(os.path.abspath(write_dir),
session_data.animal_id)
session_data._set_output_dir_(output_dir)
current_dir = os.getcwd()
os.chdir(output_dir)
output_files = []
#######################################
# Correct functional for slice timing #
#######################################
if slice_timing:
out_tshift = tshift(in_file=func_filename,
outputtype='NIFTI_GZ',
tpattern='altplus',
tr=str(t_r),
environ=environ)
func_filename = out_tshift.outputs.out_file
output_files.append(func_filename)
################################################
# Register functional volumes to the first one #
################################################
# XXX why do you need a thresholded image ?
out_clip_level = clip_level(in_file=func_filename)
out_calc_threshold = calc(in_file_a=func_filename,
expr='ispositive(a-{0}) * a'.format(
out_clip_level.outputs.clip_val),
outputtype='NIFTI_GZ')
thresholded_filename = out_calc_threshold.outputs.out_file
out_volreg = volreg( # XXX dfile not saved
in_file=thresholded_filename,
outputtype='NIFTI_GZ',
environ=environ,
oned_file=fname_presuffix(thresholded_filename,
suffix='Vr.1Dfile.1D',
use_ext=False),
oned_matrix_save=fname_presuffix(thresholded_filename,
suffix='Vr.aff12.1D',
use_ext=False))
# Apply the registration to the whole head
out_allineate = allineate(in_file=func_filename,
master=func_filename,
in_matrix=out_volreg.outputs.oned_matrix_save,
out_file=fname_presuffix(func_filename,
suffix='Av'),
environ=environ)
# 3dAllineate removes the obliquity. This is not a good way to readd it as
# removes motion correction info in the header if it were an AFNI file...as
# it happens it's NIfTI which does not store that so irrelevant!
out_copy_geom = copy_geom(dest_file=out_allineate.outputs.out_file,
in_file=out_volreg.outputs.out_file)
allineated_filename = out_copy_geom.outputs.out_file
# Create a (hopefully) nice mean image for use in the registration
out_tstat = tstat(in_file=allineated_filename,
args='-mean',
outputtype='NIFTI_GZ',
environ=environ)
# Update outputs
output_files.extend([
thresholded_filename, out_volreg.outputs.oned_matrix_save,
out_volreg.outputs.out_file, out_volreg.outputs.md1d_file,
allineated_filename, out_tstat.outputs.out_file
])
###########################################
# Corret anat and func for intensity bias #
###########################################
# Correct the functional average for intensities bias
out_bias_correct = bias_correct(input_image=out_tstat.outputs.out_file)
unbiased_func_filename = out_bias_correct.outputs.output_image
# Bias correct the antomical image
out_unifize = unifize(in_file=anat_filename,
outputtype='NIFTI_GZ',
environ=environ)
unbiased_anat_filename = out_unifize.outputs.out_file
# Update outputs
output_files.extend([unbiased_func_filename, unbiased_anat_filename])
#############################################
# Rigid-body registration anat -> mean func #
#############################################
if prior_rigid_body_registration:
# Mask the mean functional volume outside the brain.
out_clip_level = clip_level(in_file=unbiased_func_filename)
out_compute_mask_func = compute_mask(
in_file=unbiased_func_filename,
volume_threshold=brain_volume,
intensity_threshold=int(out_clip_level.outputs.clip_val))
out_cacl_func = calc(in_file_a=unbiased_func_filename,
in_file_b=out_compute_mask_func.outputs.out_file,
expr='a*b',
outputtype='NIFTI_GZ',
environ=environ)
# Mask the anatomical volume outside the brain.
out_clip_level = clip_level(in_file=unbiased_anat_filename)
out_compute_mask_anat = compute_mask(
in_file=unbiased_anat_filename,
volume_threshold=brain_volume,
intensity_threshold=int(out_clip_level.outputs.clip_val))
out_cacl_anat = calc(in_file_a=unbiased_anat_filename,
in_file_b=out_compute_mask_anat.outputs.out_file,
expr='a*b',
outputtype='NIFTI_GZ',
environ=environ)
# Compute the transformation from functional to anatomical brain
# XXX: why in this sense
out_allineate = allineate2(
in_file=out_cacl_func.outputs.out_file,
reference=out_cacl_anat.outputs.out_file,
out_matrix=fname_presuffix(out_cacl_func.outputs.out_file,
suffix='_shr.aff12.1D',
use_ext=False),
center_of_mass='',
warp_type='shift_rotate',
out_file=fname_presuffix(out_cacl_func.outputs.out_file,
suffix='_shr'),
environ=environ)
rigid_transform_file = out_allineate.outputs.out_matrix
output_files.extend([
out_compute_mask_func.outputs.out_file,
out_cacl_func.outputs.out_file,
out_compute_mask_anat.outputs.out_file,
out_cacl_anat.outputs.out_file, rigid_transform_file,
out_allineate.outputs.out_file
])
# apply the inverse transform to register the anatomical to the func
catmatvec_out_file = fname_presuffix(rigid_transform_file,
suffix='INV')
out_catmatvec = catmatvec(in_file=[(rigid_transform_file, 'I')],
oneline=True,
out_file=catmatvec_out_file)
output_files.append(out_catmatvec.outputs.out_file)
out_allineate = allineate(in_file=unbiased_anat_filename,
master=unbiased_func_filename,
in_matrix=out_catmatvec.outputs.out_file,
out_file=fname_presuffix(
unbiased_anat_filename,
suffix='_shr_in_func_space'),
environ=environ)
allineated_anat_filename = out_allineate.outputs.out_file
output_files.append(allineated_anat_filename)
else:
allineated_anat_filename = unbiased_anat_filename
############################################
# Nonlinear registration anat -> mean func #
############################################
# 3dWarp doesn't put the obliquity in the header, so do it manually
# This step generates one file per slice and per time point, so we are
# making sure they are removed at the end
out_warp = warp(in_file=allineated_anat_filename,
oblique_parent=unbiased_func_filename,
interp='quintic',
gridset=unbiased_func_filename,
outputtype='NIFTI_GZ',
verbose=True,
environ=environ)
registered_anat_filename = out_warp.outputs.out_file
registered_anat_oblique_filename = fix_obliquity(registered_anat_filename,
unbiased_func_filename,
verbose=verbose)
# Concatenate all the anat to func tranforms
mat_filename = fname_presuffix(registered_anat_filename,
suffix='_warp.mat',
use_ext=False)
# XXX Handle this correctly according to caching
if not os.path.isfile(mat_filename):
np.savetxt(mat_filename, [out_warp.runtime.stdout], fmt='%s')
output_files.append(mat_filename)
transform_filename = fname_presuffix(registered_anat_filename,
suffix='_anat_to_func.aff12.1D',
use_ext=False)
if prior_rigid_body_registration:
_ = catmatvec(in_file=[(mat_filename, 'ONELINE'),
(rigid_transform_file, 'ONELINE')],
oneline=True,
out_file=transform_filename)
else:
_ = catmatvec(in_file=[(mat_filename, 'ONELINE')],
oneline=True,
out_file=transform_filename)
##################################################
# Per-slice non-linear registration func -> anat #
##################################################
# Slice anatomical image
anat_img = nibabel.load(registered_anat_oblique_filename)
anat_n_slices = anat_img.header.get_data_shape()[2]
sliced_registered_anat_filenames = []
for slice_n in range(anat_n_slices):
out_slicer = slicer(in_file=registered_anat_oblique_filename,
keep='{0} {0}'.format(slice_n),
out_file=fname_presuffix(
registered_anat_oblique_filename,
suffix='Sl%d' % slice_n),
environ=environ)
oblique_slice = fix_obliquity(out_slicer.outputs.out_file,
registered_anat_oblique_filename,
verbose=verbose)
sliced_registered_anat_filenames.append(oblique_slice)
# Slice mean functional
sliced_bias_corrected_filenames = []
img = nibabel.load(func_filename)
n_slices = img.header.get_data_shape()[2]
for slice_n in range(n_slices):
out_slicer = slicer(in_file=unbiased_func_filename,
keep='{0} {0}'.format(slice_n),
out_file=fname_presuffix(unbiased_func_filename,
suffix='Sl%d' % slice_n),
environ=environ)
oblique_slice = fix_obliquity(out_slicer.outputs.out_file,
unbiased_func_filename,
verbose=verbose)
sliced_bias_corrected_filenames.append(oblique_slice)
# Below line is to deal with slices where there is no signal (for example
# rostral end of some anatomicals)
# The inverse warp frequently fails, Resampling can help it work better
# XXX why specifically .1 in voxel_size ?
voxel_size_z = anat_img.header.get_zooms()[2]
resampled_registered_anat_filenames = []
for sliced_registered_anat_filename in sliced_registered_anat_filenames:
out_resample = resample(in_file=sliced_registered_anat_filename,
voxel_size=(voxel_size_x, voxel_size_y,
voxel_size_z),
outputtype='NIFTI_GZ',
environ=environ)
resampled_registered_anat_filenames.append(
out_resample.outputs.out_file)
resampled_bias_corrected_filenames = []
for sliced_bias_corrected_filename in sliced_bias_corrected_filenames:
out_resample = resample(in_file=sliced_bias_corrected_filename,
voxel_size=(voxel_size_x, voxel_size_y,
voxel_size_z),
outputtype='NIFTI_GZ',
environ=environ)
resampled_bias_corrected_filenames.append(
out_resample.outputs.out_file)
# single slice non-linear functional to anatomical registration
warped_slices = []
warp_filenames = []
for (resampled_bias_corrected_filename,
resampled_registered_anat_filename) in zip(
resampled_bias_corrected_filenames,
resampled_registered_anat_filenames):
warped_slice = fname_presuffix(resampled_bias_corrected_filename,
suffix='_qw')
out_qwarp = qwarp(
in_file=resampled_bias_corrected_filename,
base_file=resampled_registered_anat_filename,
iwarp=True, # XXX: is this necessary
noneg=True,
blur=[0],
nmi=True,
noXdis=True,
allineate=True,
allineate_opts='-parfix 1 0 -parfix 2 0 -parfix 3 0 '
'-parfix 4 0 -parfix 5 0 -parfix 6 0 '
'-parfix 7 0 -parfix 9 0 '
'-parfix 10 0 -parfix 12 0',
out_file=warped_slice,
environ=environ)
warped_slices.append(out_qwarp.outputs.warped_source)
warp_filenames.append(out_qwarp.outputs.source_warp)
output_files.append(out_qwarp.outputs.base_warp)
# There are files geenrated by the allineate option
output_files.extend([
fname_presuffix(out_qwarp.outputs.warped_source, suffix='_Allin'),
fname_presuffix(out_qwarp.outputs.warped_source,
suffix='_Allin.nii',
use_ext=False),
fname_presuffix(out_qwarp.outputs.warped_source,
suffix='_Allin.aff12.1D',
use_ext=False)
])
# Resample the mean volume back to the initial resolution,
voxel_size = nibabel.load(unbiased_func_filename).header.get_zooms()
resampled_warped_slices = []
for warped_slice in warped_slices:
out_resample = resample(in_file=warped_slice,
voxel_size=voxel_size,
outputtype='NIFTI_GZ',
environ=environ)
resampled_warped_slices.append(out_resample.outputs.out_file)
# fix the obliquity
resampled_warped_slices_oblique = []
for (sliced_registered_anat_filename,
resampled_warped_slice) in zip(sliced_registered_anat_filenames,
resampled_warped_slices):
oblique_slice = fix_obliquity(resampled_warped_slice,
sliced_registered_anat_filename,
verbose=verbose)
resampled_warped_slices_oblique.append(oblique_slice)
# slice functional
sliced_func_filenames = []
for slice_n in range(n_slices):
out_slicer = slicer(in_file=allineated_filename,
keep='{0} {0}'.format(slice_n),
out_file=fname_presuffix(allineated_filename,
suffix='Sl%d' % slice_n),
environ=environ)
oblique_slice = fix_obliquity(out_slicer.outputs.out_file,
allineated_filename,
verbose=verbose)
sliced_func_filenames.append(oblique_slice)
# Apply the precomputed warp slice by slice
warped_func_slices = []
for (sliced_func_filename, warp_filename) in zip(sliced_func_filenames,
warp_filenames):
out_warp_apply = warp_apply(in_file=sliced_func_filename,
master=sliced_func_filename,
warp=warp_filename,
out_file=fname_presuffix(
sliced_func_filename, suffix='_qw'),
environ=environ)
warped_func_slices.append(out_warp_apply.outputs.out_file)
# Finally, merge all slices !
out_merge_func = merge(in_files=warped_func_slices,
outputtype='NIFTI_GZ',
environ=environ)
# Fix the obliquity
merged_oblique = fix_obliquity(out_merge_func.outputs.out_file,
allineated_filename,
verbose=verbose)
# Update the fmri data
setattr(session_data, "coreg_func_", merged_oblique)
setattr(session_data, "coreg_anat_", registered_anat_oblique_filename)
setattr(session_data, "coreg_transform_", transform_filename)
os.chdir(current_dir)
# Collect the outputs
output_files.extend(sliced_registered_anat_filenames +
sliced_bias_corrected_filenames +
resampled_registered_anat_filenames +
resampled_bias_corrected_filenames + warped_slices +
warp_filenames + resampled_warped_slices_oblique +
sliced_func_filenames + warped_func_slices)
if not caching:
for out_file in output_files:
if os.path.isfile(out_file):
os.remove(out_file)
def func_to_anat(func_filename, anat_filename, tr, write_dir, caching=False):
"""
The functional volume is aligned to the anatomical, first with a rigid body
registration and then on a per-slice basis (only a fine correction, this is
mostly for correction of EPI distortion). This pipeline includes
slice timing.
"""
if caching:
memory = Memory(write_dir)
tshift = memory.cache(afni.TShift)
clip_level = memory.cache(afni.ClipLevel)
threshold = memory.cache(fsl.Threshold)
volreg = memory.cache(afni.Volreg)
allineate = memory.cache(afni.Allineate)
copy_geom = memory.cache(fsl.CopyGeom)
bias_correct = memory.cache(ants.N4BiasFieldCorrection)
tstat = memory.cache(afni.TStat)
rats = memory.cache(RatsMM)
calc = memory.cache(afni.Calc)
allineate = memory.cache(afni.Allineate)
allineate2 = memory.cache(afni.Allineate)
unifize = memory.cache(afni.Unifize)
catmatvec = memory.cache(afni.CatMatvec)
warp = memory.cache(afni.Warp)
resample = memory.cache(afni.Resample)
slicer = memory.cache(afni.ZCutUp)
warp_apply = memory.cache(afni.NwarpApply)
qwarp = memory.cache(afni.Qwarp)
merge = memory.cache(fsl.Merge)
else:
tshift = afni.TShift().run
clip_level = afni.ClipLevel().run
threshold = fsl.Threshold().run
volreg = afni.Volreg().run
allineate = afni.Allineate().run
allineate2 = afni.Allineate().run # TODO: remove after fixed bug
copy_geom = fsl.CopyGeom().run
bias_correct = ants.N4BiasFieldCorrection().run
tstat = afni.TStat().run
rats = RatsMM().run
calc = afni.Calc().run
allineate = afni.Allineate().run
unifize = afni.Unifize().run
catmatvec = afni.CatMatvec().run
warp = afni.Warp().run
resample = afni.Resample().run
slicer = afni.ZCutUp().run
warp_apply = afni.NwarpApply().run
qwarp = afni.Qwarp().run
merge = fsl.Merge().run
# Correct slice timing
os.chdir(write_dir)
out_tshift = tshift(in_file=func_filename,
outputtype='NIFTI_GZ',
tpattern='altplus',
tr=str(tr))
tshifted_filename = out_tshift.outputs.out_file
# Register to the first volume
# XXX why do you need a thresholded image ?
out_clip_level = clip_level(in_file=tshifted_filename)
out_threshold = threshold(in_file=tshifted_filename,
thresh=out_clip_level.outputs.clip_val)
thresholded_filename = out_threshold.outputs.out_file
oned_filename = fname_presuffix(thresholded_filename,
suffix='Vr.1Dfile.1D',
use_ext=False)
oned_matrix_filename = fname_presuffix(thresholded_filename,
suffix='Vr.aff12.1D',
use_ext=False)
out_volreg = volreg(
in_file=thresholded_filename,
outputtype='NIFTI_GZ',
oned_file=oned_filename, # XXX dfile not saved
oned_matrix_save=oned_matrix_filename)
# XXX: bad output: up and down on y-axis
# Apply the registration to the whole head
allineated_filename = fname_presuffix(tshifted_filename, suffix='Av')
out_allineate = allineate(in_file=tshifted_filename,
master=tshifted_filename,
in_matrix=out_volreg.outputs.oned_matrix_save,
out_file=allineated_filename)
# 3dAllineate removes the obliquity. This is not a good way to readd it as
# removes motion correction info in the header if it were an AFNI file...as
# it happens it's NIfTI which does not store that so irrelevant!
out_copy_geom = copy_geom(dest_file=out_allineate.outputs.out_file,
in_file=out_volreg.outputs.out_file)
allineated_filename = out_copy_geom.outputs.out_file
# XXX: bad output: up and down on y-axis
# Create a (hopefully) nice mean image for use in the registration
out_tstat = tstat(in_file=allineated_filename,
args='-mean',
outputtype='NIFTI_GZ')
averaged_filename = out_tstat.outputs.out_file
# Correct the functional average for intensities bias
out_bias_correct = bias_correct(input_image=averaged_filename, dimension=3)
unbiased_func_filename = out_bias_correct.outputs.output_image
# Bias correct the antomical image
out_unifize = unifize(in_file=anat_filename, outputtype='NIFTI_GZ')
unbiased_anat_filename = out_unifize.outputs.out_file
# Mask the mean functional volume outside the brain.
out_clip_level = clip_level(in_file=unbiased_func_filename)
# XXX bad: brain mask cut
out_rats = rats(in_file=unbiased_func_filename,
volume_threshold=400,
intensity_threshold=int(out_clip_level.outputs.clip_val))
out_cacl = calc(in_file_a=unbiased_func_filename,
in_file_b=out_rats.outputs.out_file,
expr='a*b',
outputtype='NIFTI_GZ')
# Compute the transformation from the functional image to the anatomical
# XXX: why in this sense
out_allineate = allineate2(
in_file=out_cacl.outputs.out_file,
reference=unbiased_anat_filename,
out_matrix=fname_presuffix(out_cacl.outputs.out_file,
suffix='_shr.aff12.1D',
use_ext=False),
center_of_mass='',
warp_type='shift_rotate',
out_file=fname_presuffix(out_cacl.outputs.out_file, suffix='_shr'))
rigid_transform_file = out_allineate.outputs.out_matrix
# apply the inverse transformation to register to the anatomical volume
catmatvec_out_file = fname_presuffix(rigid_transform_file, suffix='INV')
if not os.path.isfile(catmatvec_out_file):
_ = catmatvec(in_file=[(rigid_transform_file, 'I')],
oneline=True,
out_file=catmatvec_out_file)
# XXX not cached I don't understand why
out_allineate = allineate(in_file=unbiased_anat_filename,
master=unbiased_func_filename,
in_matrix=catmatvec_out_file,
out_file=fname_presuffix(
unbiased_anat_filename,
suffix='_shr_in_func_space'))
# suppanatwarp="$base"_BmBe_shr.aff12.1D
# Non-linear registration
# XXX what is the difference between Warp and 3dQwarp?
out_warp = warp(in_file=out_allineate.outputs.out_file,
oblique_parent=unbiased_func_filename,
interp='quintic',
gridset=unbiased_func_filename,
outputtype='NIFTI_GZ',
verbose=True)
registered_anat_filename = out_warp.outputs.out_file
mat_filename = fname_presuffix(registered_anat_filename,
suffix='_warp.mat',
use_ext=False)
if not os.path.isfile(mat_filename):
np.savetxt(mat_filename, [out_warp.runtime.stdout], fmt='%s')
# 3dWarp doesn't put the obliquity in the header, so do it manually
# This step generates one file per slice and per time point, so we are
# making sure they are removed at the end
registered_anat_oblique_filename = fix_obliquity(registered_anat_filename,
unbiased_func_filename,
overwrite=False)
# Slice anatomical image
anat_img = nibabel.load(registered_anat_oblique_filename)
anat_n_slices = anat_img.header.get_data_shape()[2]
sliced_registered_anat_filenames = []
for slice_n in range(anat_n_slices):
out_slicer = slicer(in_file=registered_anat_oblique_filename,
keep='{0} {1}'.format(slice_n, slice_n),
out_file=fname_presuffix(
registered_anat_oblique_filename,
suffix='Sl%d' % slice_n))
sliced_registered_anat_filenames.append(out_slicer.outputs.out_file)
# Slice mean functional
sliced_bias_corrected_filenames = []
img = nibabel.load(func_filename)
n_slices = img.header.get_data_shape()[2]
for slice_n in range(n_slices):
out_slicer = slicer(in_file=unbiased_func_filename,
keep='{0} {1}'.format(slice_n, slice_n),
out_file=fname_presuffix(unbiased_func_filename,
suffix='Sl%d' % slice_n))
sliced_bias_corrected_filenames.append(out_slicer.outputs.out_file)
# Below line is to deal with slices where there is no signal (for example
# rostral end of some anatomicals)
# The inverse warp frequently fails, Resampling can help it work better
voxel_size_z = anat_img.header.get_zooms()[2]
resampled_registered_anat_filenames = []
for sliced_registered_anat_filename in sliced_registered_anat_filenames:
out_resample = resample(in_file=sliced_registered_anat_filename,
voxel_size=(.1, .1, voxel_size_z),
outputtype='NIFTI_GZ')
resampled_registered_anat_filenames.append(
out_resample.outputs.out_file)
resampled_bias_corrected_filenames = []
for sliced_bias_corrected_filename in sliced_bias_corrected_filenames:
out_resample = resample(in_file=sliced_bias_corrected_filename,
voxel_size=(.1, .1, voxel_size_z),
outputtype='NIFTI_GZ')
resampled_bias_corrected_filenames.append(
out_resample.outputs.out_file)
# single slice non-linear functional to anatomical registration
warped_slices = []
warp_filenames = []
for (resampled_bias_corrected_filename,
resampled_registered_anat_filename) in zip(
resampled_bias_corrected_filenames,
resampled_registered_anat_filenames):
warped_slice = fname_presuffix(resampled_bias_corrected_filename,
suffix='_qw')
out_qwarp = qwarp(in_file=resampled_bias_corrected_filename,
base_file=resampled_registered_anat_filename,
iwarp=True,
noneg=True,
blur=[0],
nmi=True,
noXdis=True,
allineate=True,
allineate_opts='-parfix 1 0 -parfix 2 0 -parfix 3 0 '
'-parfix 4 0 -parfix 5 0 -parfix 6 0 '
'-parfix 7 0 -parfix 9 0 '
'-parfix 10 0 -parfix 12 0',
out_file=warped_slice)
warped_slices.append(out_qwarp.outputs.warped_source)
warp_filenames.append(out_qwarp.outputs.source_warp)
# Resample the mean volume back to the initial resolution,
voxel_size = nibabel.load(
sliced_bias_corrected_filename).header.get_zooms()
resampled_warped_slices = []
for warped_slice in warped_slices:
out_resample = resample(in_file=warped_slice,
voxel_size=voxel_size + (voxel_size[0], ),
outputtype='NIFTI_GZ')
resampled_warped_slices.append(out_resample.outputs.out_file)
# fix the obliquity
for (resampled_registered_anat_filename,
resampled_warped_slice) in zip(resampled_registered_anat_filenames,
resampled_warped_slices):
_ = fix_obliquity(resampled_warped_slice,
resampled_registered_anat_filename)
# Merge all slices !
# out_merge_mean = merge(in_files=resampled_warped_slices, dimension='z')
# slice functional
sliced_func_filenames = []
for slice_n in range(n_slices):
out_slicer = slicer(in_file=allineated_filename,
keep='{0} {1}'.format(slice_n, slice_n),
out_file=fname_presuffix(allineated_filename,
suffix='Sl%d' % slice_n))
sliced_func_filenames.append(out_slicer.outputs.out_file)
# resample functional slices
resampled_func_filenames = []
for sliced_func_filename in sliced_func_filenames:
out_resample = resample(in_file=sliced_func_filename,
voxel_size=(.1, .1, voxel_size_z),
outputtype='NIFTI_GZ')
resampled_func_filenames.append(out_resample.outputs.out_file)
# Apply the precomputed warp slice by slice
warped_func_slices = []
for (resampled_func_filename,
warp_filename) in zip(resampled_func_filenames, warp_filenames):
out_warp_apply = warp_apply(in_file=resampled_func_filename,
warp=warp_filename,
out_file=fname_presuffix(
resampled_func_filename, suffix='_qw'))
warped_func_slices.append(out_warp_apply.outputs.out_file)
# Fix the obliquity
# XXX why no resampling back before ?
for (resampled_registered_anat_filename,
warped_func_slice) in zip(resampled_registered_anat_filenames,
warped_func_slices):
_ = fix_obliquity(warped_func_slice,
resampled_registered_anat_filename)
# Finally, merge all slices !
out_merge_func = merge(in_files=warped_func_slices, dimension='z')
out_merge_anat = merge(in_files=resampled_registered_anat_filenames,
dimension='z')
return (out_merge_func.outputs.merged_file,
out_merge_anat.outputs.merged_file)
def _realign(func_filename,
write_dir,
caching=False,
terminal_output='allatonce',
environ=None):
if environ is None:
environ = {'AFNI_DECONFLICT': 'OVERWRITE'}
if caching:
memory = Memory(write_dir)
clip_level = memory.cache(afni.ClipLevel)
threshold = memory.cache(fsl.Threshold)
volreg = memory.cache(afni.Volreg)
allineate = memory.cache(afni.Allineate)
copy = memory.cache(afni.Copy)
copy_geom = memory.cache(fsl.CopyGeom)
tstat = memory.cache(afni.TStat)
for step in [threshold, volreg, allineate, tstat, copy, copy_geom]:
step.interface().set_default_terminal_output(terminal_output)
else:
clip_level = afni.ClipLevel().run
threshold = fsl.Threshold(terminal_output=terminal_output).run
volreg = afni.Volreg(terminal_output=terminal_output).run
allineate = afni.Allineate(terminal_output=terminal_output).run
copy = afni.Copy(terminal_output=terminal_output).run
copy_geom = fsl.CopyGeom(terminal_output=terminal_output).run
tstat = afni.TStat(terminal_output=terminal_output).run
out_clip_level = clip_level(in_file=func_filename)
out_threshold = threshold(in_file=func_filename,
thresh=out_clip_level.outputs.clip_val,
out_file=fname_presuffix(func_filename,
suffix='_thresholded',
newpath=write_dir))
thresholded_filename = out_threshold.outputs.out_file
out_volreg = volreg( # XXX dfile not saved
in_file=thresholded_filename,
out_file=fname_presuffix(thresholded_filename,
suffix='_volreg',
newpath=write_dir),
environ=environ,
oned_file=fname_presuffix(thresholded_filename,
suffix='_volreg.1Dfile.1D',
use_ext=False,
newpath=write_dir),
oned_matrix_save=fname_presuffix(thresholded_filename,
suffix='_volreg.aff12.1D',
use_ext=False,
newpath=write_dir))
# Apply the registration to the whole head
out_allineate = allineate(in_file=func_filename,
master=func_filename,
in_matrix=out_volreg.outputs.oned_matrix_save,
out_file=fname_presuffix(func_filename,
suffix='_volreg',
newpath=write_dir),
environ=environ)
# 3dAllineate removes the obliquity. This is not a good way to readd it as
# removes motion correction info in the header if it were an AFNI file...as
# it happens it's NIfTI which does not store that so irrelevant!
out_copy = copy(in_file=out_allineate.outputs.out_file,
out_file=fname_presuffix(out_allineate.outputs.out_file,
suffix='_oblique',
newpath=write_dir),
environ=environ)
out_copy_geom = copy_geom(dest_file=out_copy.outputs.out_file,
in_file=out_volreg.outputs.out_file)
oblique_allineated_filename = out_copy_geom.outputs.out_file
# Create a (hopefully) nice mean image for use in the registration
out_tstat = tstat(in_file=oblique_allineated_filename,
args='-mean',
out_file=fname_presuffix(oblique_allineated_filename,
suffix='_tstat',
newpath=write_dir),
environ=environ)
# Remove intermediate outputs
if not caching:
for output_file in [
thresholded_filename, out_volreg.outputs.oned_matrix_save,
out_volreg.outputs.out_file, out_volreg.outputs.md1d_file,
out_allineate.outputs.out_file
]:
os.remove(output_file)
return (oblique_allineated_filename, out_tstat.outputs.out_file,
out_volreg.outputs.oned_file)