def mask2subjspace_real(mnimask, anat, pe, mni2anat_hd5, affine_matrix, workdir):
"""
Simulate data based on transformation matrices already obtained
from analysis of real data.
(This is the same as mask2pe_ants in extract_pe.py for extracting parameter estimates).
"""
"""
paths for temporary files and output file
"""
# temporary nifti file
mni2anat_out_name = join(workdir, 'mnimask2anat.nii.gz')
# inverse affine transform
affine_matrix_inverse = join(workdir, 'anat2pe.txt')
# path to output file
outfile = join(workdir, 'mask2pe.nii.gz')
"""
Invert affine and apply both transforms
"""
# invert affine transmatrix (output from glm analysis)
inverse = ConvertXFM(
in_file=affine_matrix,
out_file=affine_matrix_inverse,
invert_xfm=True)
inverse.run()
# apply inverse transform from mni to anat space
# (output from glm analysis)
mni2anat = ants.ApplyTransforms(
input_image=mnimask,
reference_image=anat,
output_image=mni2anat_out_name,
transforms=[mni2anat_hd5],
dimension=3, interpolation='NearestNeighbor',
terminal_output='file')
mni2anat.run()
# apply inverse affine transform from anat to pe estimate space
mni2pe = fsl.FLIRT(
interp='nearestneighbour',
apply_xfm=True,
in_matrix_file=affine_matrix_inverse,
out_matrix_file=join(workdir, 'anat2pe_flirt.mat'),
# the above output matrix is redundant. But if we don't specify,
# it just gets stored next to the script (and overwritten when
# iterating over subjects!). We want it tidy.
in_file=mni2anat_out_name,
reference=pe,
out_file=outfile)
mni2pe.run()
# return path to projected mask
return outfile
def mask2pe(
pe,
anat,
mnimask,
workdir,
standard='/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz'
):
"""
Compute new 2-step projection for a masn from mni to 3D parameter space (and apply it).
"""
# create transformation matrix from mni to anatomical
mni2anat = fsl.FLIRT(dof=12,
interp='trilinear',
in_file=standard,
reference=anat,
out_file=join(workdir, 'mni2anat.nii.gz'),
out_matrix_file=join(workdir, 'mni2anat.txt'))
mni2anat.run()
# anat to parameter estimate map (3D statistical volume)
anat2pe = fsl.FLIRT(dof=6,
interp='trilinear',
in_file=anat,
reference=pe,
out_file=join(workdir, 'anat2pe.nii.gz'),
out_matrix_file=join(workdir, 'anat2pe.txt'))
anat2pe.run()
# concatinate matrices
concat = ConvertXFM(concat_xfm=True,
in_file2=join(workdir, 'mni2anat.txt'),
in_file=join(workdir, 'anat2pe.txt'),
out_file=join(workdir, 'mni2pe.txt'))
concat.run()
# set path to output file
outfile = join(workdir, 'mask2pe.nii.gz')
# apply transformation to mask image
mni2pe = fsl.FLIRT(interp='nearestneighbour',
apply_xfm=True,
in_matrix_file=join(workdir, 'mni2pe.txt'),
out_matrix_file=join(workdir, 'mask2pe.txt'),
in_file=mnimask,
reference=pe,
out_file=outfile)
mni2pe.run()
# return path to transformed result
return outfile
def mni2bold(bold, anat, standard, mask, workdir):
"""
Use fsl.FLIRT to transform a mask from MNI to subject space
"""
os.makedirs(workdir)
# bold to anat
bold2anat = fsl.FLIRT(dof=6,
no_clamp=True,
in_file=bold,
reference=anat,
out_matrix_file=join(workdir, 'bold2anat.txt'),
out_file=join(workdir, 'bold2anat.nii.gz'))
bold2anat.run()
# anat to mni
anat2mni = fsl.FLIRT(dof=12,
in_file=anat,
reference=standard,
out_matrix_file=join(workdir, 'anat2mni.txt'),
out_file=join(workdir, sub, run,
'%s_%s_anat2mni.nii.gz' % (sub, run)))
anat2mni.run()
# concatinate matrices
concat = ConvertXFM(concat_xfm=True,
in_file2=join(workdir, sub, run,
'%s_%s_bold2anat.txt' % (sub, run)),
in_file=join(workdir, sub, run,
'%s_%s_anat2mni.txt' % (sub, run)),
out_file=join(workdir, sub, run,
'%s_%s_bold2mni.txt' % (sub, run)))
concat.run()
# inverse transmatrix
inverse = ConvertXFM(in_file=join(workdir, sub, run,
'%s_%s_bold2mni.txt' % (sub, run)),
out_file=join(workdir, sub, run,
'%s_%s_mni2bold.txt' % (sub, run)),
invert_xfm=True)
inverse.run()
# apply to mask
mni2bold = fsl.FLIRT(
interp='nearestneighbour',
apply_xfm=True,
in_matrix_file=join(workdir, sub, run,
'%s_%s_mni2bold.txt' % (sub, run)),
in_file=join(mask),
reference=join(data_basedir, sub, 'BOLD', run, 'bold.nii.gz'),
out_file=join(workdir, sub, run, '%s_%s_roimask.nii.gz' % (sub, run)))
mni2bold.run()
mask_subjspace = join(workdir, sub, run,
'%s_%s_roimask.nii.gz' % (sub, run))
# return path of created mask
return mask_subjspace
def mask2subjspace(sub, run, data_basedir, workdir, mask):
"""
Use fsl.FLIRT to transform roi mask from MNI to subject space
(without brain extraction).
"""
from nipype.interfaces import fsl
from nipype.interfaces.fsl.utils import ConvertXFM
from os.path import join
import os
os.makedirs(join(workdir, sub, run))
# bold to anat
bold2anat = fsl.FLIRT(
dof=6, no_clamp=True,
in_file=join(data_basedir, sub, 'BOLD', run, 'bold.nii.gz'),
reference=join(data_basedir, sub, 'anatomy', 'highres001.nii.gz'),
out_matrix_file=join(workdir, sub, run, '%s_%s_bold2anat.txt' % (sub, run)),
out_file=join(workdir, sub, run, '%s_%s_bold2anat.nii.gz' % (sub, run)))
bold2anat.run()
# anat to mni
anat2mni = fsl.FLIRT(
dof=12, interp='nearestneighbour',
in_file=join(data_basedir, sub, 'anatomy', 'highres001.nii.gz'),
reference='/usr/share/fsl/5.0//data/standard/MNI152_T1_2mm_brain.nii.gz',
out_matrix_file=join(workdir, sub, run, '%s_%s_anat2mni.txt' % (sub, run)),
out_file=join(workdir, sub, run, '%s_%s_anat2mni.nii.gz' % (sub, run)))
anat2mni.run()
# concatinate matrices
concat = ConvertXFM(
concat_xfm=True,
in_file2=join(workdir, sub, run, '%s_%s_bold2anat.txt' % (sub, run)),
in_file=join(workdir, sub, run, '%s_%s_anat2mni.txt' % (sub, run)),
out_file=join(workdir, sub, run, '%s_%s_bold2mni.txt' % (sub, run)))
concat.run()
# inverse transmatrix
inverse = ConvertXFM(
in_file=join(workdir, sub, run, '%s_%s_bold2mni.txt' % (sub, run)),
out_file=join(workdir, sub, run, '%s_%s_mni2bold.txt' % (sub, run)),
invert_xfm=True)
inverse.run()
# apply to mask
mni2bold = fsl.FLIRT(
interp='nearestneighbour',
apply_xfm=True,
in_matrix_file=join(workdir, sub, run, '%s_%s_mni2bold.txt' % (sub, run)),
in_file=join(mask),
reference=join(data_basedir, sub, 'BOLD', run, 'bold.nii.gz'),
out_file=join(workdir, sub, run, '%s_%s_roimask.nii.gz' % (sub, run)))
mni2bold.run()
mask_subjspace = join(workdir, sub, run, '%s_%s_roimask.nii.gz' % (sub, run))
# return path of created mask
return mask_subjspace
def test_ConvertXFM_outputs():
output_map = dict(out_file=dict(), )
outputs = ConvertXFM.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_ConvertXFM_outputs():
output_map = dict(out_file=dict(),
)
outputs = ConvertXFM.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_ConvertXFM_inputs():
input_map = dict(
args=dict(argstr='%s', ),
concat_xfm=dict(
argstr='-concat',
position=-3,
requires=['in_file2'],
xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'],
),
environ=dict(
nohash=True,
usedefault=True,
),
fix_scale_skew=dict(
argstr='-fixscaleskew',
position=-3,
requires=['in_file2'],
xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'],
),
ignore_exception=dict(
nohash=True,
usedefault=True,
),
in_file=dict(
argstr='%s',
mandatory=True,
position=-1,
),
in_file2=dict(
argstr='%s',
position=-2,
),
invert_xfm=dict(
argstr='-inverse',
position=-3,
xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'],
),
out_file=dict(
argstr='-omat %s',
genfile=True,
hash_files=False,
position=1,
),
output_type=dict(),
terminal_output=dict(
mandatory=True,
nohash=True,
),
)
inputs = ConvertXFM.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def test_ConvertXFM_inputs():
input_map = dict(args=dict(argstr='%s',
),
concat_xfm=dict(argstr='-concat',
position=-3,
requires=['in_file2'],
xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'],
),
environ=dict(nohash=True,
usedefault=True,
),
fix_scale_skew=dict(argstr='-fixscaleskew',
position=-3,
requires=['in_file2'],
xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'],
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
in_file=dict(argstr='%s',
mandatory=True,
position=-1,
),
in_file2=dict(argstr='%s',
position=-2,
),
invert_xfm=dict(argstr='-inverse',
position=-3,
xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'],
),
out_file=dict(argstr='-omat %s',
genfile=True,
hash_files=False,
position=1,
),
output_type=dict(),
terminal_output=dict(mandatory=True,
nohash=True,
),
)
inputs = ConvertXFM.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def mask2bold(
bold,
anat,
roi_mask,
workdir,
standard='/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz'
):
"""
Project a mask image to individual subject space. anatomical image must
be defined for registration. workdir is needed to dump temporary files
created by fsl. output is a nifti image.
"""
from os.path import join
import os
# create workdir
if not os.path.exists(workdir):
print('working directory did not exist and is created now.')
os.makedirs(workdir)
# produce matrix for bold2anat
bold2anat = fsl.FLIRT(dof=6,
interp='trilinear',
in_file=bold,
reference=anat,
out_file=join(workdir, 'bold2anat.nii.gz'),
out_matrix_file=join(workdir, 'bold2anat.txt'))
bold2anat.run()
# anat to mni
anat2mni = fsl.FLIRT(dof=12,
interp='trilinear',
in_file=anat,
reference=standard,
out_file=join(workdir, 'anat2mni.nii.gz'),
out_matrix_file=join(workdir, 'anat2mni.txt'))
anat2mni.run()
# concatinate matrices
concat = ConvertXFM(concat_xfm=True,
in_file2=join(workdir, 'bold2anat.txt'),
in_file=join(workdir, 'anat2mni.txt'),
out_file=join(workdir, 'bold2mni.txt'))
concat.run()
# inverse transmatrix
inverse = ConvertXFM(in_file=join(workdir, 'bold2mni.txt'),
out_file=join(workdir, 'mni2bold.txt'),
invert_xfm=True)
inverse.run()
# apply to mask
mni2bold = fsl.FLIRT(interp='nearestneighbour',
apply_xfm=True,
in_matrix_file=join(workdir, 'mni2bold.txt'),
out_matrix_file=join(workdir, 'roimask.txt'),
in_file=roi_mask,
reference=bold,
out_file=join(workdir, 'roimask.nii.gz'))
mni2bold.run()
mask_subspace_path = join(workdir, 'roimask.nii.gz')
# TODO: registration fails pretty much ...
return mask_subspace_path
def fix_preparation_pipeline(self, **kwargs):
pipeline = self.create_pipeline(
name='prepare_fix',
inputs=[
DatasetSpec('melodic_ica', directory_format),
DatasetSpec('filtered_data', nifti_gz_format),
DatasetSpec('coreg_to_atlas_mat', text_matrix_format),
DatasetSpec('coreg_matrix', text_matrix_format),
DatasetSpec('preproc', nifti_gz_format),
DatasetSpec('brain', nifti_gz_format),
DatasetSpec('coreg_ref_brain', nifti_gz_format),
DatasetSpec('mc_par', par_format),
DatasetSpec('brain_mask', nifti_gz_format)
],
outputs=[
DatasetSpec('fix_dir', directory_format),
DatasetSpec('hand_label_noise', text_format)
],
desc=("Pipeline to create the right folder structure before "
"running FIX"),
version=1,
citations=[fsl_cite],
**kwargs)
struct_ants2fsl = pipeline.create_node(ANTs2FSLMatrixConversion(),
name='struct_ants2fsl',
requirements=[c3d_req])
struct_ants2fsl.inputs.ras2fsl = True
struct_ants2fsl.inputs.reference_file = self.parameter('MNI_template')
pipeline.connect_input('coreg_to_atlas_mat', struct_ants2fsl,
'itk_file')
pipeline.connect_input('coreg_ref_brain', struct_ants2fsl,
'source_file')
epi_ants2fsl = pipeline.create_node(ANTs2FSLMatrixConversion(),
name='epi_ants2fsl',
requirements=[c3d_req])
epi_ants2fsl.inputs.ras2fsl = True
pipeline.connect_input('brain', epi_ants2fsl, 'source_file')
pipeline.connect_input('coreg_matrix', epi_ants2fsl, 'itk_file')
pipeline.connect_input('coreg_ref_brain', epi_ants2fsl,
'reference_file')
MNI2t1 = pipeline.create_node(ConvertXFM(),
name='MNI2t1',
wall_time=5,
requirements=[fsl509_req])
MNI2t1.inputs.invert_xfm = True
pipeline.connect(struct_ants2fsl, 'fsl_matrix', MNI2t1, 'in_file')
struct2epi = pipeline.create_node(ConvertXFM(),
name='struct2epi',
wall_time=5,
requirements=[fsl509_req])
struct2epi.inputs.invert_xfm = True
pipeline.connect(epi_ants2fsl, 'fsl_matrix', struct2epi, 'in_file')
meanfunc = pipeline.create_node(ImageMaths(op_string='-Tmean',
suffix='_mean'),
name='meanfunc',
wall_time=5,
requirements=[fsl509_req])
pipeline.connect_input('preproc', meanfunc, 'in_file')
prep_fix = pipeline.create_node(PrepareFIX(), name='prep_fix')
pipeline.connect_input('melodic_ica', prep_fix, 'melodic_dir')
pipeline.connect_input('coreg_ref_brain', prep_fix, 't1_brain')
pipeline.connect_input('mc_par', prep_fix, 'mc_par')
pipeline.connect_input('brain_mask', prep_fix, 'epi_brain_mask')
pipeline.connect_input('preproc', prep_fix, 'epi_preproc')
pipeline.connect_input('filtered_data', prep_fix, 'filtered_epi')
pipeline.connect(epi_ants2fsl, 'fsl_matrix', prep_fix, 'epi2t1_mat')
pipeline.connect(struct_ants2fsl, 'fsl_matrix', prep_fix, 't12MNI_mat')
pipeline.connect(MNI2t1, 'out_file', prep_fix, 'MNI2t1_mat')
pipeline.connect(struct2epi, 'out_file', prep_fix, 't12epi_mat')
pipeline.connect(meanfunc, 'out_file', prep_fix, 'epi_mean')
pipeline.connect_output('fix_dir', prep_fix, 'fix_dir')
pipeline.connect_output('hand_label_noise', prep_fix,
'hand_label_file')
return pipeline
def fix_preparation_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='prepare_fix',
desc=("Pipeline to create the right folder structure before "
"running FIX"),
citations=[fsl_cite],
name_maps=name_maps)
if self.branch('coreg_to_tmpl_method', 'ants'):
struct_ants2fsl = pipeline.add(
'struct_ants2fsl',
ANTs2FSLMatrixConversion(ras2fsl=True),
inputs={
'reference_file': ('template_brain', nifti_gz_format),
'itk_file': ('coreg_to_tmpl_ants_mat', text_matrix_format),
'source_file': ('coreg_ref_brain', nifti_gz_format)
},
requirements=[c3d_req.v('1.0.0')])
struct_matrix = (struct_ants2fsl, 'fsl_matrix')
else:
struct_matrix = ('coreg_to_tmpl_fsl_mat', text_matrix_format)
# if self.branch('coreg_method', 'ants'):
# epi_ants2fsl = pipeline.add(
# 'epi_ants2fsl',
# ANTs2FSLMatrixConversion(
# ras2fsl=True),
# inputs={
# 'source_file': ('brain', nifti_gz_format),
# 'itk_file': ('coreg_ants_mat', text_matrix_format),
# 'reference_file': ('coreg_ref_brain', nifti_gz_format)},
# requirements=[c3d_req.v('1.0.0')])
MNI2t1 = pipeline.add('MNI2t1',
ConvertXFM(invert_xfm=True),
inputs={'in_file': struct_matrix},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
struct2epi = pipeline.add(
'struct2epi',
ConvertXFM(invert_xfm=True),
inputs={'in_file': ('coreg_fsl_mat', text_matrix_format)},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
meanfunc = pipeline.add(
'meanfunc',
ImageMaths(op_string='-Tmean',
suffix='_mean',
output_type='NIFTI_GZ'),
inputs={'in_file': ('series_preproc', nifti_gz_format)},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
pipeline.add('prep_fix',
PrepareFIX(),
inputs={
'melodic_dir': ('melodic_ica', directory_format),
't1_brain': ('coreg_ref_brain', nifti_gz_format),
'mc_par': ('mc_par', par_format),
'epi_brain_mask': ('brain_mask', nifti_gz_format),
'epi_preproc': ('series_preproc', nifti_gz_format),
'filtered_epi': ('filtered_data', nifti_gz_format),
'epi2t1_mat': ('coreg_fsl_mat', text_matrix_format),
't12MNI_mat': (struct_ants2fsl, 'fsl_matrix'),
'MNI2t1_mat': (MNI2t1, 'out_file'),
't12epi_mat': (struct2epi, 'out_file'),
'epi_mean': (meanfunc, 'out_file')
},
outputs={
'fix_dir': ('fix_dir', directory_format),
'hand_label_noise': ('hand_label_file', text_format)
})
return pipeline
def hybrid_rois_registration(base_dir,
subject_id,
visit_id,
output_dir,
csf_roi,
wm_roi,
template="MNI152_T1_2mm.nii.gz",
dof=6,
output_type="NIFTI"):
"""Function to register csf and wm roi from template to diffusion space and output the MEDIAN signal within the roi. Needed for hybrid Beltrami FW fitting
Parameters
----------
base_dir : absolute path pointing at the root directory of the bids repository
subject_id: string, the tag subject (i.e. sub-sublabel) of the subject to treat
visit_id: the VALUE of the session tag to be treated (i.e. for ses-02, only "02" need to be entered)
output_dir: absolute path of the directories were the indexes will be written
csf_roi: absolute path of the roi representative of the csf. It should be in the same space as "template" and binary
wm_roi: absolute path of the roi representative of the wm. It should be in in the same space as "template" and binary
template: name of the file with extension of the template to be used for inverse registation of the rois.
output_type: ["NIFTI", "NIFTI_GZ"], the type of nifti output desired,
... : other parameters related to the dipy functions used
Returns
----------
csf_mean, wm_mean: floats. The median csf and wm values from the registered ROIs
"""
diff_dir = "{}/{}/ses-{}/dwi".format(base_dir, subject_id, visit_id)
anat_dir = "{}/{}/ses-{}/anat".format(base_dir, subject_id, visit_id)
if output_type == "NIFTI":
ext = ".nii"
elif output_type == "NIFTI_GZ":
ext = ".nii.gz"
else:
raise ValueError(
"Output file type {} not recognized".format(output_type))
t1_file = glob("{}/*T1w.nii*".format(anat_dir))[0]
t1_base_name = get_base_name_all_type(t1_file)
diff_file = glob("{}/*dwi.nii*".format(diff_dir))[0]
diff_base_name = get_base_name_all_type(diff_file)
fsldir_system = subprocess.check_output("echo $FSLDIR", shell=True)
if type(fsldir_system) == bytes:
fsl_dir = fsldir_system.decode("utf-8").rstrip()
else:
fsl_dir = fsldir_system.rstrip()
template_base_name = get_base_name_all_type(template)
template_no_underscore = "x".join(template_base_name.split("_"))
template_abs = "{}/data/standard/{}".format(fsl_dir, template)
flirt = FLIRT()
#T1 to template
print("Registering T1 onto template")
flirt.inputs.in_file = t1_file
flirt.inputs.reference = template_abs
flirt.inputs.out_file = "{}/{}_ref-{}_dof-12_reg-flirt{}".format(
output_dir, t1_base_name, template_no_underscore, ext)
flirt.inputs.out_matrix_file = "{}/{}_ref-{}_dof-12_reg-flirt.mat".format(
output_dir, t1_base_name, template_no_underscore)
flirt.inputs.output_type = output_type
flirt.run()
#diff to t1
print("Registering diffusion onto T1")
flirt.inputs.in_file = diff_file
flirt.inputs.reference = t1_file
flirt.inputs.dof = dof
flirt.inputs.out_file = "{}/{}_ref-t1_dof-{}_reg-flirt{}".format(
output_dir, diff_base_name, str(dof), ext)
flirt.inputs.out_matrix_file = "{}/{}_ref-t1_dof-{}_reg-flirt.mat".format(
output_dir, diff_base_name, str(dof))
flirt.inputs.output_type = output_type
flirt.run()
#concat and inverse matrices
print("Concat and inverse matrix, send rois to diff")
mat_transform = ConvertXFM()
#concat diff to t1 and t1 to template
mat_transform.inputs.in_file = "{}/{}_ref-{}_dof-12_reg-flirt.mat".format(
output_dir, t1_base_name, template_no_underscore)
mat_transform.inputs.in_file2 = "{}/{}_ref-t1_dof-{}_reg-flirt.mat".format(
output_dir, diff_base_name, str(dof))
mat_transform.inputs.concat_xfm = True
mat_transform.inputs.out_file = "{}/diff_to_{}.mat".format(
output_dir, template_no_underscore)
mat_transform.run()
#inverse
mat_transform = ConvertXFM()
mat_transform.inputs.in_file = "{}/diff_to_{}.mat".format(
output_dir, template_no_underscore)
mat_transform.inputs.invert_xfm = True
mat_transform.inputs.out_file = "{}/{}_to_diff.mat".format(
output_dir, template_no_underscore)
mat_transform.run()
#send csf and wm roi to diff
csf_roi_base_name = get_base_name_all_type(csf_roi)
wm_roi_base_name = get_base_name_all_type(wm_roi)
#csf
flirt.inputs.in_file = csf_roi
flirt.inputs.reference = diff_file
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = "{}/{}_to_diff.mat".format(
output_dir, template_no_underscore)
flirt.inputs.interp = "nearestneighbour"
flirt.inputs.output_type = output_type
flirt.inputs.out_file = "{}/{}_in_diff{}".format(output_dir,
csf_roi_base_name, ext)
flirt.run()
#wm
flirt.inputs.in_file = wm_roi
flirt.inputs.reference = diff_file
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = "{}/{}_to_diff.mat".format(
output_dir, template_no_underscore)
flirt.inputs.interp = "nearestneighbour"
flirt.inputs.output_type = output_type
flirt.inputs.out_file = "{}/{}_in_diff{}".format(output_dir,
wm_roi_base_name, ext)
flirt.run()
#extract values from roi
csf_image = nb.load("{}/{}_in_diff{}".format(output_dir, csf_roi_base_name,
ext))
csf_array = csf_image.get_fdata()
csf_array_mask = np.where(csf_array == 1)
wm_image = nb.load("{}/{}_in_diff{}".format(output_dir, wm_roi_base_name,
ext))
wm_array = wm_image.get_fdata()
wm_array_mask = np.where(wm_array == 1)
diff_image = nb.load(diff_file)
b0_array = diff_image.get_fdata()[:, :, :, 0]
csf_mean = np.median(b0_array[csf_array_mask])
wm_mean = np.median(b0_array[wm_array_mask])
return (csf_mean, wm_mean)
def registration_pipeline(self, **kwargs): # @UnusedVariable @IgnorePep8
"""
Register T1 and T2 to the
Parameters
----------
"""
pipeline = self.create_pipeline(
name='registration_pipeline',
inputs=[
DatasetSpec('ute_echo1', dicom_format),
DatasetSpec('ute_echo2', dicom_format)
],
outputs=[
DatasetSpec('ute1_registered', nifti_format),
DatasetSpec('ute2_registered', nifti_gz_format),
DatasetSpec('template_to_ute_mat', text_matrix_format),
DatasetSpec('ute_to_template_mat', text_matrix_format)
],
desc="Register ute images to the template",
version=1,
citations=(fsl_cite),
**kwargs)
echo1_conv = pipeline.create_node(MRConvert(), name='echo1_conv')
echo1_conv.inputs.out_ext = '.nii.gz'
pipeline.connect_input('ute_echo1', echo1_conv, 'in_file')
echo2_conv = pipeline.create_node(MRConvert(), name='echo2_conv')
echo2_conv.inputs.out_ext = '.nii.gz'
pipeline.connect_input('ute_echo2', echo2_conv, 'in_file')
# Create registration node
registration = pipeline.create_node(FLIRT(),
name='ute1_registration',
requirements=[fsl5_req],
wall_time=180)
pipeline.connect(echo1_conv, 'out_file', registration, 'in_file')
registration.inputs.reference = self.template_path
registration.inputs.output_type = 'NIFTI_GZ'
registration.inputs.searchr_x = [-180, 180]
registration.inputs.searchr_y = [-180, 180]
registration.inputs.searchr_z = [-180, 180]
registration.inputs.bins = 256
registration.inputs.cost_func = 'corratio'
# Inverse matrix conversion
convert_mat = pipeline.create_node(ConvertXFM(),
name='inverse_matrix_conversion',
requirements=[fsl5_req],
wall_time=10)
pipeline.connect(registration, 'out_matrix_file', convert_mat,
'in_file')
convert_mat.inputs.invert_xfm = True
# UTE_echo_2 transformation
transform_ute2 = pipeline.create_node(ApplyXFM(),
name='transform_t2',
requirements=[fsl5_req],
wall_time=10)
pipeline.connect(registration, 'out_matrix_file', transform_ute2,
'in_matrix_file')
pipeline.connect(echo2_conv, 'out_file', transform_ute2, 'in_file')
transform_ute2.inputs.output_type = 'NIFTI_GZ'
transform_ute2.inputs.reference = self.template_path
transform_ute2.inputs.apply_xfm = True
# Connect outputs
pipeline.connect_output('ute1_registered', registration, 'out_file')
pipeline.connect_output('ute_to_template_mat', registration,
'out_matrix_file')
pipeline.connect_output('ute2_registered', transform_ute2, 'out_file')
pipeline.connect_output('template_to_ute_mat', convert_mat, 'out_file')
pipeline.assert_connected()
return pipeline