def create_mni2diff_transforms(bedpostx_dir):
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
####Custom inputs####
try:
FSLDIR = os.environ['FSLDIR']
except NameError:
print('FSLDIR environment variable not set!')
merged_f_samples_path = bedpostx_dir + '/merged_f1samples.nii.gz'
####Custom inputs####
print('\nCreating MNI-diffusion space transforms...\n')
input_MNI = FSLDIR + '/data/standard/MNI152_T1_1mm_brain.nii.gz'
out_aff = bedpostx_dir + '/xfms/MNI2diff_affine.nii.gz'
##Create transform matrix between diff and MNI using FLIRT
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = merged_f_samples_path
flirt.inputs.in_file = input_MNI
flirt.inputs.out_matrix_file = bedpostx_dir + '/xfms/MNI2diff.mat'
flirt.inputs.out_file = '/tmp/out_flirt.nii.gz'
flirt.run()
##Apply transform between diff and MNI using FLIRT
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = merged_f_samples_path
flirt.inputs.in_file = input_MNI
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = bedpostx_dir + '/xfms/MNI2diff.mat'
flirt.inputs.out_file = out_aff
flirt.inputs.out_matrix_file = '/tmp/out_flirt.mat'
flirt.run()
return out_aff
def _apply_coregistration(item, reference_item, input_dir, tmp_dir, output_dir):
"""Coregisters all items to the reference item. The reference item is skipped in the list of items.
Args:
item (str): the items base_name to register to the reference item
reference_item (str): the name of the reference item in the items list
input_dir (str): the input directory in which the items reside
tmp_dir (str): the working dir. Outputs reference volume and reference matrix
"""
reference_mean_b0 = os.path.join(tmp_dir, reference_item + '_mask.nii.gz')
reference_dwi = os.path.join(input_dir, reference_item + '.nii.gz')
input_mean_b0 = os.path.join(tmp_dir, item + '_mask.nii.gz')
input_dwi = os.path.join(input_dir, item + '.nii.gz')
out_b0_vol = os.path.join(tmp_dir, item + '_to_' + reference_item + '_mean_b0.nii.gz')
out_img = os.path.join(output_dir, item + '.nii.gz')
out_mat = os.path.join(tmp_dir, item + '_to_' + reference_item + '_mean_b0.mat')
flirt_b0 = pe.Node(fsl.FLIRT(in_file=input_mean_b0, reference=reference_mean_b0,
out_file=out_b0_vol, out_matrix_file=out_mat, dof=6),
name='flirt_b0')
flirt_b0.run()
flirt_apply = pe.Node(fsl.FLIRT(in_file=input_dwi, reference=reference_dwi,
out_file=out_img, in_matrix_file=out_mat,
apply_xfm=True),
name='flirt')
flirt_apply.run()
def epi_normalize(name='epi_normalize'):
inputnode = pe.Node(
utility.IdentityInterface(
fields=['fmri_mean','t1','t1_to_mni','t1_mask']),
name='inputspec')
outputnode = pe.Node(
utility.IdentityInterface(
fields=['epi2t1_warp','coregistered_fmri_mean','epi2mni_warp',
't1_to_epi_warp','epi_mask']),
name='outputspec')
n_spm_coregister = pe.Node(
spm.Coregister(jobtype='estimate'),
name='spm_coregister')
# n_epi2mni = pe.Node(
# spm.preprocess.ApplyDeformations(
# reference_volume='/coconut/applis/src/spm8_x64/toolbox/Seg/TPM.nii'),
# name='epi2mni')
n_flirt_epi2t1 = pe.Node(
fsl.FLIRT(out_matrix_file='flirt_epi2t1.mat',
out_file='%s_flirt',
cost='normmi', # as in fcon1000 preproc, why??
searchr_x=[-10,10],searchr_y=[-10,10],searchr_z=[-10,10],
dof=6),
name='flirt_epi2t1')
n_t1_to_epi = pe.Node(
fsl.ConvertXFM(invert_xfm=True),
name='t1_to_epi')
n_mask_to_epi = pe.Node(
fsl.FLIRT(interp='nearestneighbour',
out_file='%s_epi',
apply_xfm=True,),
name='mask_to_epi')
w=pe.Workflow(name=name)
w.connect([
# (inputnode,n_spm_coregister,[('fmri_mean','source'),
# ('t1','target')]),
(inputnode,n_flirt_epi2t1,[('t1','reference')]),
# (n_spm_coregister,n_epi2mni,[('coregistered_source','in_files')]),
# (inputnode,n_epi2mni,[('t1_to_mni','deformation_field')]),
(inputnode,n_flirt_epi2t1,[('fmri_mean','in_file')]),
(n_flirt_epi2t1,outputnode,[('out_matrix_file','epi2t1_warp')]),
(n_flirt_epi2t1,n_t1_to_epi,[('out_matrix_file','in_file')]),
(n_t1_to_epi,outputnode,[('out_file','t1_to_epi_warp')]),
(inputnode,n_mask_to_epi,[('fmri_mean','reference'),
('t1_mask','in_file')]),
(n_t1_to_epi, n_mask_to_epi,[('out_file','in_matrix_file')]),
(n_mask_to_epi, outputnode, [('out_file','epi_mask')])
# (n_spm_coregister,outputnode,[('coregistered_source',
# 'coregistered_fmri_mean')]),
])
return w
def build_nodes(self):
# BET - Skullstrip anatomical Image
self.bet_anat = Node(fsl.BET(frac=0.5,
robust=True,
output_type='NIFTI_GZ'),
name="bet_anat")
# image segmentation
self.segmentation = Node(fsl.FAST(output_type='NIFTI_GZ'), name='segmentation')
# threshold WM probability image
self.threshold = Node(fsl.Threshold(thresh=0.5,
args='-bin',
output_type='NIFTI_GZ'),
name='threshold')
# flirt - pre-alignment of images
self.coreg_pre = Node(fsl.FLIRT(dof=6, output_type='NIFTI_GZ'), name='coreg_pre')
# co-reg
self.coreg_mi = Node(fsl.FLIRT(bins=640, cost_func='bbr', interp='spline', searchr_x=[-180, 180],
searchr_y=[-180, 180], searchr_z=[-180, 180], dof=6, output_type='NIFTI_GZ'),
name='coreg_mi')
# apply warp map to images
self.applywarp = Node(fsl.preprocess.ApplyXFM(apply_xfm=True,
output_type='NIFTI_GZ'),
name='applywarp')
# Apply coregistration warp to mean file
self.applywarp_mean = Node(fsl.FLIRT(interp='spline',output_type='NIFTI_GZ'), name="applywarp_mean")
def quick_transform(c):
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
import nipype.interfaces.fsl as fsl
wf = pe.Workflow(name='flirt_transform')
sink = pe.Node(nio.DataSink(),name='sinker')
sink.inputs.base_directory = c.sink_dir
if c.create_transform:
datagrabber = c.datagrabber_create.create_dataflow()
infosource = datagrabber.get_node('subject_id_iterable')
xform = pe.MapNode(fsl.FLIRT(interp=c.interpolation),name='flirt',iterfield=['in_file'])
wf.connect(xform,'out_matrix_file',sink,'%s.@outmatfile'%c.name)
elif c.apply_transform:
datagrabber = c.datagrabber_apply.create_dataflow()
infosource = datagrabber.get_node('subject_id_iterable')
xform = pe.MapNode(fsl.FLIRT(interp=c.interpolation,apply_xfm=True),name='flirt',iterfield=['in_file'])
wf.connect(datagrabber,'datagrabber.reg_mat',xform,'in_matrix_file')
else:
raise Exception("Need to either create or apply a flirt transform!!")
wf.connect(datagrabber,'datagrabber.inputs',xform,'in_file')
wf.connect(datagrabber,'datagrabber.template',xform,'reference')
wf.connect(infosource,'subject_id',sink,'container')
wf.connect(xform,'out_file',sink,'%s.@outfile'%c.name)
subs = lambda sub_id: [('_subject_id_%s'%sub_id,'')]+[('_flirt%d'%i,'') for i in range(20)]
wf.connect(infosource,('subject_id', subs),sink,'substitutions')
return wf
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 epi_unwrap(name='epi_unwrap'):
inputnode = pe.Node(
utility.IdentityInterface(
fields=['fieldmap', 'fieldmap_mask', 'fieldmap_to_epi',
'epi_file','epi_reference',
'echo_time','echo_spacing','unwarp_direction']),
name='inputspec')
outputnode = pe.Node(
utility.IdentityInterface(
fields=['unwarped_epi','voxel_shift_map']),
name='outputspec')
n_fieldmap_to_epi = pe.Node(
fsl.FLIRT(apply_xfm=True,
no_resample_blur=True),
name='fieldmap_to_epi')
n_mask_to_epi = pe.Node(
fsl.FLIRT(apply_xfm=True,
interp='nearestneighbour'),
name='mask_to_epi')
n_epi_voxelshiftmap = pe.Node(
fsl.FUGUE(shift_out_file='vsm_epi.nii.gz',),
name='epi_voxelshiftmap')
n_unwarp_epi = pe.Node(
fsl.FUGUE(),
name='unwarp_epi')
w=pe.Workflow(name=name)
w.connect([
(inputnode, n_fieldmap_to_epi, [
('fieldmap_to_epi','in_matrix_file'),
('fieldmap','in_file'),
('epi_reference','reference'),]),
(inputnode, n_mask_to_epi, [
('fieldmap_to_epi','in_matrix_file'),
('fieldmap_mask','in_file'),
('epi_reference','reference'),]),
(n_fieldmap_to_epi,n_epi_voxelshiftmap,[('out_file','fmap_in_file')]),
(n_mask_to_epi, n_epi_voxelshiftmap, [('out_file','mask_file')]),
(inputnode, n_epi_voxelshiftmap,[
('epi_reference','in_file'),
('unwarp_direction','unwarp_direction'),
('echo_spacing','dwell_time')]),
(n_mask_to_epi, n_unwarp_epi, [('out_file','mask_file')]),
(n_epi_voxelshiftmap,n_unwarp_epi,[('shift_out_file','shift_in_file')]),
(inputnode,n_unwarp_epi,[
('epi_file','in_file'),]),
])
return w
def linear_registration_( self ):
"""Linear registration. First part in the study template creation. Estimation of the registration parameters of GM to grey matter standard template."""
try:
#
#
#
# Retrieve the GM tissue prior
avg152T1_gray = ""
if os.environ.get('FSLDIR'):
avg152T1_gray = os.path.join( os.environ.get('FSLDIR'),
"data","standard","tissuepriors", "avg152T1_gray.hdr" )
else:
raise Exception( "$FSLDIR env variable is not setup on your system" )
#
# Loop on the tasks
while True:
# get the item
item = self.queue_[0].get()
# registration estimation
flt = fsl.FLIRT()
flt.inputs.in_file = os.path.join( self.maps_dir_, item )
flt.inputs.reference = avg152T1_gray
flt.inputs.out_file = os.path.join( self.template_dir_, "%s_li_MNI.nii.gz"%item[:-7] )
flt.inputs.out_matrix_file = os.path.join( self.template_dir_, "%s_li_MNI.mat"%item[:-7] )
flt.inputs.dof = 12
res = flt.run()
# apply registration
flt = fsl.FLIRT()
flt.inputs.in_file = os.path.join( self.maps_dir_, item )
flt.inputs.reference = avg152T1_gray
flt.inputs.out_file = os.path.join( self.template_dir_, "%s_li_MNI.nii.gz"%item[:-7] )
flt.inputs.in_matrix_file = os.path.join( self.template_dir_, "%s_li_MNI.mat"%item[:-7] )
flt.inputs.out_matrix_file = os.path.join( self.template_dir_, "%s_li_MNI_apply.mat"%item[:-7] )
flt.inputs.apply_xfm = True
flt.inputs.dof = 12
res = flt.run()
# lock and add the file
singlelock.acquire()
self.linear_MNI_.append( flt.inputs.out_file )
singlelock.release()
# job is done
self.queue_[0].task_done()
#
#
except Exception as inst:
print inst
_log.error(inst)
quit(-1)
except IOError as e:
print "I/O error({0}): {1}".format(e.errno, e.strerror)
quit(-1)
except:
print "Unexpected error:", sys.exc_info()[0]
quit(-1)
def flirt_registration(self, keepfiles=False):
"""
"""
def _ssos(data):
"""Squared sum of squares from multichannel complex data"""
ssos = np.sqrt(np.mean(np.absolute(data), axis=self.rcvrdim))
return ssos
# make workdir if does not exist
if not os.path.exists(self.workdir):
os.makedirs(self.workdir)
# make 6d nifti data for flirt affine transform
img_6d = vj.util.make_6d(self.imgspace)
# making niftis
img_out = self.workdir + '/composer_img_main'
ref_out = self.workdir + '/composer_ref_main'
flirt_out = self.workdir + '/composer_flirtout'
full = self.workdir + '/composer_6d_img'
writer = vj.io.NiftiWriter(_ssos(self.imgspace), self.procpar,\
input_space='local',\
output_space='scanner')
writer.write(img_out)
writer = vj.io.NiftiWriter(_ssos(self.imgspace_ref), self.procpar_ref,\
input_space='local',\
output_space='scanner')
writer.write(ref_out)
writer = vj.io.NiftiWriter(img_6d, self.procpar_ref,\
input_space='local',\
output_space='scanner')
writer.write(full)
# registering by combined magnitude FSL FLIRT
flirt = fsl.FLIRT()
flirt.inputs.in_file = img_out + '.nii.gz'
flirt.inputs.reference = ref_out + '.nii.gz'
flirt.inputs.out_file = flirt_out + '.nii.gz'
flirt.inputs.out_matrix_file = 'composer_invol2refvolmat'
print(flirt.cmdline)
res = flirt.run()
# applying the resulting transform to full data
flirt = fsl.FLIRT()
flirt.inputs.in_file = img_out + '.nii.gz'
flirt.inputs.reference = ref_out + '.nii.gz'
flirt.inputs.out_file = flirt_out + '.nii.gz'
flirt.inputs.out_matrix_file = 'composer_invol2refvolmat'
print(flirt.cmdline)
vj.io.NiftiReader(flirt_out + '.nii.gz')
# loading result nifti
rdr = vj.io.NiftiReader(flirt_out + '.nii.gz')
def coreg_vent_CSF_to_diff(dwi_dir, csf_loc, mni_csf_loc):
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
print('\nTransforming CSF mask to diffusion space...')
merged_f_samples_path = "%s%s" % (dwi_dir, '/merged_f1samples.nii.gz')
if os.path.exists(merged_f_samples_path) is True:
dwi_infile = merged_f_samples_path
else:
dwi_infile = "%s%s" % (dwi_dir, '/dwi.nii.gz')
csf_mask_diff_out = "%s%s" % (dwi_dir, '/csf_diff.nii.gz')
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = dwi_infile
flirt.inputs.in_file = csf_loc
flirt.inputs.out_file = csf_mask_diff_out
flirt.inputs.out_matrix_file = '/tmp/out_flirt.mat'
flirt.inputs.in_matrix_file = "%s%s" % (dwi_dir, '/xfms/MNI2diff.mat')
flirt.inputs.apply_xfm = True
flirt.run()
vent_mask_diff_out = dwi_dir + '/ventricle_diff.nii.gz'
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = dwi_infile
flirt.inputs.in_file = mni_csf_loc
flirt.inputs.out_file = vent_mask_diff_out
flirt.inputs.out_matrix_file = '/tmp/out_flirt.mat'
flirt.inputs.in_matrix_file = "%s%s" % (dwi_dir, '/xfms/MNI2diff.mat')
flirt.inputs.apply_xfm = True
flirt.run()
# Mask CSF with MNI ventricle mask
print('Masking CSF with ventricle mask...')
vent_csf_diff_out = "%s%s" % (dwi_dir, '/vent_csf_diff.nii.gz')
args = "%s%s" % ('-mas ', vent_mask_diff_out)
maths = fsl.ImageMaths(in_file=csf_mask_diff_out,
op_string=args,
out_file=vent_csf_diff_out)
os.system(maths.cmdline)
print('Eroding and binarizing CSF mask...')
# Erode CSF mask
out_file_final = "%s%s" % (vent_csf_diff_out.split('.nii.gz')[0],
'_ero.nii.gz')
args = '-ero -bin'
maths = fsl.ImageMaths(in_file=vent_csf_diff_out,
op_string=args,
out_file=out_file_final)
os.system(maths.cmdline)
return out_file_final
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 init_fsl(self, in_file: str, ref: str, out_file: str, out_mat: str):
ax = fsl.FLIRT()
ax.inputs.in_file = in_file
ax.inputs.reference = ref
ax.inputs.out_file = out_file
ax.inputs.out_matrix_file = out_mat
return ax
def create_workflow():
workflow = Workflow(
name='transform_manual_mask')
inputs = Node(IdentityInterface(fields=[
'subject_id',
'session_id',
'refsubject_id',
'ref_funcmask',
'ref_func',
'funcs',
]), name='in')
# Find the transformation matrix func_ref -> func
# First find transform from func to manualmask's ref func
# first take the median (flirt functionality has changed and no longer automatically takes the first volume when given 4D files)
median_func = MapNode(
interface=fsl.maths.MedianImage(dimension="T"),
name='median_func',
iterfield=('in_file'),
)
findtrans = MapNode(fsl.FLIRT(),
iterfield=['in_file'],
name='findtrans'
)
# Invert the matrix transform
invert = MapNode(fsl.ConvertXFM(invert_xfm=True),
name='invert',
iterfield=['in_file'],
)
workflow.connect(findtrans, 'out_matrix_file',
invert, 'in_file')
# Transform the manualmask to be aligned with func
funcreg = MapNode(ApplyXFMRefName(),
name='funcreg',
iterfield=['in_matrix_file', 'reference'],
)
workflow.connect(inputs, 'funcs',
median_func, 'in_file')
workflow.connect(median_func, 'out_file',
findtrans, 'in_file')
workflow.connect(inputs, 'ref_func',
findtrans, 'reference')
workflow.connect(invert, 'out_file',
funcreg, 'in_matrix_file')
workflow.connect(inputs, 'ref_func',
funcreg, 'in_file')
workflow.connect(inputs, 'funcs',
funcreg, 'reference')
return workflow
def reg_parcels2diff(dwi_dir, seeds_dir):
import re
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
merged_f_samples_path = "%s%s" % (dwi_dir, '/merged_f1samples.nii.gz')
if os.path.exists(merged_f_samples_path) is True:
dwi_infile = merged_f_samples_path
else:
dwi_infile = "%s%s" % (dwi_dir, '/dwi.nii.gz')
seeds_list = [i for i in os.listdir(seeds_dir) if '.nii' in i]
def atoi(text):
return int(text) if text.isdigit() else text
def natural_keys(text):
return [atoi(c) for c in re.split('(\d+)', text)]
seeds_list.sort(key=natural_keys)
i = 0
for parcel in seeds_list:
out_file = "%s%s%s%s" % (seeds_dir, '/region_', str(i), '_diff.nii.gz')
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = dwi_infile
flirt.inputs.in_file = "%s%s%s" % (seeds_dir, '/', parcel)
flirt.inputs.out_file = out_file
flirt.inputs.out_matrix_file = '/tmp/out_flirt.mat'
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = "%s%s" % (dwi_dir, '/xfms/MNI2diff.mat')
flirt.run()
i = i + 1
seeds_list = [i for i in os.listdir(seeds_dir) if 'diff.nii' in i]
return seeds_list
def autorotate(
template,
in_file='structural.nii',
):
"""Multi-rotation-state transformation start. This allows the registration to commence with the best rotational fit, and may help if the orientation of the data is malformed with respect to the header.
Parameters
----------
template : string
Full path to template data.
in_file : string
Name of input NIfTI file with data which is to be transformed.
Returns
-------
flt_res : Path names of output_file, out_log, and out_matrix_file (affine transformation).
"""
flt = fsl.FLIRT(bins=640, cost_func='mutualinfo')
flt.inputs.in_file = in_file
flt.inputs.reference = template
flt.inputs.output_type = "NIFTI_GZ"
flt.inputs.dof = 6
flt.input.searchr_x = [-180, 180]
flt.input.searchr_y = [-180, 180]
flt.input.searchr_z = [-180, 180]
flt.input.force_scaling = True
flt.cmdline
flt_res = flt.run()
return flt_res
def epi_sbref_registration(name='EPI_SBrefRegistration'):
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(fields=['epi_brain', 'sbref_brain']),
name='inputnode')
outputnode = pe.Node(
niu.IdentityInterface(fields=['epi_registered', 'out_mat']),
name='outputnode')
mean = pe.Node(fsl.MeanImage(dimension='T'), name='EPImean')
inu = pe.Node(ants.N4BiasFieldCorrection(dimension=3), name='EPImeanBias')
epi_sbref = pe.Node(fsl.FLIRT(dof=6, out_matrix_file='init.mat'),
name='EPI2SBRefRegistration')
epi_split = pe.Node(fsl.Split(dimension='t'), name='EPIsplit')
epi_xfm = pe.MapNode(fsl.ApplyXfm(),
name='EPIapplyxfm',
iterfield=['in_file'])
epi_merge = pe.Node(fsl.Merge(dimension='t'), name='EPImergeback')
workflow.connect([
(inputnode, epi_split, [('epi_brain', 'in_file')]),
(inputnode, epi_sbref, [('sbref_brain', 'reference')]),
(inputnode, epi_xfm, [('sbref_brain', 'reference')]),
(inputnode, mean, [('epi_brain', 'in_file')]),
(mean, inu, [('out_file', 'input_image')]),
(inu, epi_sbref, [('output_image', 'in_file')]),
(epi_split, epi_xfm, [('out_files', 'in_file')]),
(epi_sbref, epi_xfm, [('out_matrix_file', 'in_matrix_file')]),
(epi_xfm, epi_merge, [('out_file', 'in_files')]),
(epi_sbref, outputnode, [('out_matrix_file', 'out_mat')]),
(epi_merge, outputnode, [('merged_file', 'epi_registered')])
])
return workflow
def apply_xfm_node(config: dict, **kwargs):
'''
Parses config file to return desired apply_xfm node.
Parameters
----------
config : dict
PALS config file
kwargs
Keyword arguments to send to registration method.
Returns
-------
MapNode
'''
if (not config['Analysis']['Registration']):
# No registration; no xfm to apply.
n = MapNode(Function(function=infile_to_outfile,
input_names=['in_file', 'in_matrix_file'],
output_names='out_file'),
name='transformation_skip',
iterfield=['in_file', 'in_matrix_file'])
else:
n = MapNode(fsl.FLIRT(apply_xfm=True,
reference=config['Registration']['reference']),
name='transformation_flirt',
iterfield=['in_file', 'in_matrix_file'])
return n
def registration_node(config: dict, **kwargs):
'''
Parses config file to return desired registration method.
Parameters
----------
config : dict
PALS config file
kwargs
Keyword arguments to send to registration method.
Returns
-------
MapNode
'''
# Get registration method
reg_method = config['Analysis']['RegistrationMethod']
if (not config['Analysis']['Registration']):
# No registration; in -> out
n = MapNode(Function(function=reg_no_reg,
input_names=['in_file'],
output_names=['out_file', 'out_matrix_file']),
name='registration_identity',
iterfield='in_file')
elif (reg_method.lower() == 'flirt'):
# Use FLIRT
n = MapNode(fsl.FLIRT(),
name='registration_flirt',
iterfield='in_file')
for k, v in kwargs.items():
setattr(n.inputs, k, v)
else:
raise (NotImplementedError(
f'Registration method {reg_method} not implemented.'))
return n
def registration(in_file, out_file, reference):
fsl.FSLCommand.set_default_output_type('NIFTI')
flt = fsl.FLIRT(bins=640, cost_func='mutualinfo')
flt.inputs.in_file = in_file
flt.inputs.out_file = out_file
flt.inputs.reference = reference
result = flt.run()
def fsl_realign_opt(name='fsl_realign_opt'):
inputnode = pe.Node(
utility.IdentityInterface(
fields=['fmri','reference','mask']),
name='inputspec')
n_flirt_epi2t1 = pe.Node(
fsl.FLIRT(out_matrix_file='flirt_epi2t1.mat',
cost='normmi', # as in fcon1000 preproc, why??
searchr_x=[-10,10],searchr_y=[-10,10],searchr_z=[-10,10],
dof=6),
name='flirt_epi2t1')
n_mcflirt_spline = pe.Node(
fsl.MCFLIRT(interpolation='spline',
ref_vol=0,
save_plots=True,
save_rms=True,
save_mats=True,
stats_imgs=True,
dof=6),
name='mcflirt_spline')
w=pe.Workflow(name=name)
w.connect([
(inputnode,n_flirt_epi2t1,[('fmri','in_file'),
('reference','reference')]),
(inputnode,n_mcflirt_spline,[('fmri','in_file'),]),
(n_flirt_epi2t1,n_mcflirt_spline,[('out_matrix_file','init')])
])
return w
def func2mni_wf():
mni_skull_2mm = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm.nii.gz'
mni_brain_2mm = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz'
flow = Workflow('func2mni_nonlinear')
inputnode = Node(util.IdentityInterface(fields=['func_image',
'reference_image',
'func2anat_affine',
'anat2mni_warp']),name = 'inputnode')
outputnode = Node(util.IdentityInterface(fields=['func2mni_2mm',
'func2mni_4mm']),name = 'outputnode')
applywarp = Node(fsl.ApplyWarp(), name = 'apply_warp',)
applywarp.inputs.ref_file = mni_brain_2mm
flirt4mm = Node(fsl.FLIRT(), name = 'resample_4mm')
flirt4mm.inputs.reference = mni_brain_2mm
flirt4mm.inputs.apply_isoxfm = 4.0
flow.connect(inputnode, 'func_image' , applywarp, 'in_file')
flow.connect(inputnode, 'anat2mni_warp' , applywarp, 'field_file')
flow.connect(inputnode, 'func2anat_affine' , applywarp, 'premat')
flow.connect(applywarp, 'out_file' , flirt4mm, 'in_file')
flow.connect(applywarp, 'out_file' , outputnode, 'func2mni_2mm')
flow.connect(flirt4mm, 'out_file' , outputnode, 'func2mni_4mm')
return flow
def register_dwi_files_to_super_b0(dwi_files, super_b0 , out_dir, force_run = True):
"""
Register list of dwi files to super b0 (both paths)
"""
processed_files = []
registered_dir = os.path.join(out_dir, 'registered_dwi_files')
logger.info("Creaging dwi directory {}".format(registered_dir))
make_dir_safe(registered_dir)
flirt = fsl.FLIRT()
flirt.inputs.reference = super_b0
flirt.inputs.interp = 'sinc'
flirt.inputs.sinc_width = 7
flirt.inputs.sinc_window = 'blackman'
flirt.inputs.no_search = False
flirt.inputs.verbose = 1
flirt.inputs.padding_size = 1
flirt.inputs.output_type = 'NIFTI'
for i, dwi_file in enumerate(dwi_files):
flirt.inputs.in_file = dwi_file
flirt.inputs.out_file = os.path.join(registered_dir, "flirt-{num:02d}.nii".format(num = i+1))
processed_files.append(flirt.inputs.out_file)
flirt.inputs.out_matrix_file = os.path.join(registered_dir, "flirt-{num:02d}.txt".format(num = i+1))
if not os.path.isfile(flirt.inputs.out_matrix_file) or force_run:
flirt.run()
return processed_files
def coreg_mask_to_diff(dwi_dir, mask):
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
print('\nTransforming custom waypoint mask to diffusion space...')
merged_f_samples_path = "%s%s" % (dwi_dir, '/merged_f1samples.nii.gz')
if os.path.exists(merged_f_samples_path) is True:
dwi_infile = merged_f_samples_path
else:
dwi_infile = "%s%s" % (dwi_dir, '/dwi.nii.gz')
out_file = "%s%s" % (dwi_dir, '/mask_custom_diff.nii.gz')
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = dwi_infile
flirt.inputs.in_file = mask
flirt.inputs.out_file = out_file
flirt.inputs.out_matrix_file = '/tmp/out_flirt.mat'
flirt.inputs.in_matrix_file = "%s%s" % (dwi_dir, '/xfms/MNI2diff.mat')
flirt.inputs.apply_xfm = True
flirt.run()
args = '-bin'
maths = fsl.ImageMaths(in_file=out_file, op_string=args, out_file=out_file)
print('\nBinarizing custom mask...')
os.system(maths.cmdline)
return out_file
def linear_registration(
in_file: Path,
ref: Path,
out_file: Path,
out_mat: Path = None,
coregister: bool = False,
):
"""
Wrap inputs into FSL's FLIRT interface for linear registraions.
Parameters
----------
in_file : Path
Path to "moving" file
ref : Path
Path to reference file
out_file : Path
Path to output registered file
coregister : bool, optional
Indicating whether it's a within-subject registration, by default False
"""
if not out_mat:
in_name = in_file.name.split(".")[0]
ref_name = ref.name.split(".")[0]
out_mat = out_file.parent / f"{in_name}-{ref_name}_affine.mat"
flt = fsl.FLIRT()
flt.inputs.in_file = in_file
flt.inputs.reference = ref
flt.inputs.out_file = out_file
if coregister:
flt.inputs.cost = "mutualinfo"
flt.inputs.out_matrix_file = out_mat
return flt
def FLIRT(self, in_file: str, ref: str, out_dir: str, type: int):
"""
FLIRT linear transformation
@param in_file: image to be transformed
@param ref: image to transform into
@param out_dir: directory for outputs
@param type: 0 for highres2lowres, 1 for atlasHighres2highres, 2 for atlasLabels2highres
@return:
"""
flt = fsl.FLIRT()
flt.inputs.in_file = in_file
flt.inputs.reference = ref
flt.inputs.bins = 256
flt.inputs.cost = "corratio"
flt.inputs.searchr_x = [-90, 90]
flt.inputs.searchr_y = [-90, 90]
flt.inputs.searchr_z = [-90, 90]
flt.inputs.dof = 12
flt.inputs.interp = "trilinear"
if type == 0:
flt.inputs.out_file = f"{out_dir}/Highres2Lowres_linear.nii"
flt.inputs.out_matrix_file = f"{out_dir}/Highres2Lowres_linear.mat"
print("Running linear transformation from Highres to Lowres:")
elif type == 1:
flt.inputs.out_file = f"{out_dir}/HighresAtlas2Highres_linear.nii"
flt.inputs.out_matrix_file = f"{out_dir}/HighresAtlas2Highres_linear.mat"
print("Running linear transformation from Atlas to Highres:")
elif type == 2:
flt.inputs.out_file = f"{out_dir}/LabelsAtlas2Highres_linear.nii"
flt.inputs.out_matrix_file = f"{out_dir}/LabelsAtlas2Highres_linear.mat"
print("Running linear transformation from Atlas to Highres:")
flt.inputs.output_type = "NIFTI"
print(flt.cmdline)
flt.run()
return flt.inputs.out_matrix_file
def reg_parcels2diff(bedpostx_dir):
import re
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
merged_f_samples_path = bedpostx_dir + '/merged_f1samples.nii.gz'
volumes_dir = bedpostx_dir + '/volumes'
volumes_list = [i for i in os.listdir(volumes_dir) if '.nii' in i]
def atoi(text):
return int(text) if text.isdigit() else text
def natural_keys(text):
return [atoi(c) for c in re.split('(\d+)', text)]
volumes_list.sort(key=natural_keys)
i = 0
for parcel in volumes_list:
out_file = volumes_dir + '/region_' + str(i) + '_diff.nii.gz'
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = merged_f_samples_path
flirt.inputs.in_file = volumes_dir + '/' + parcel
flirt.inputs.out_file = out_file
flirt.inputs.out_matrix_file = '/tmp/out_flirt.mat'
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = bedpostx_dir + '/xfms/MNI2diff.mat'
flirt.run()
i = i + 1
volumes_list = [i for i in os.listdir(volumes_dir) if 'diff.nii' in i]
return volumes_list
def create_eddy_correct_pipeline(name='eddy_correct'):
"""
.. deprecated:: 0.9.3
Use :func:`nipype.workflows.dmri.preprocess.epi.ecc_pipeline` instead.
Creates a pipeline that replaces eddy_correct script in FSL. It takes a
series of diffusion weighted images and linearly co-registers them to one
reference image. No rotation of the B-matrix is performed, so this pipeline
should be executed after the motion correction pipeline.
Example
-------
>>> nipype_eddycorrect = create_eddy_correct_pipeline('nipype_eddycorrect')
>>> nipype_eddycorrect.inputs.inputnode.in_file = 'diffusion.nii'
>>> nipype_eddycorrect.inputs.inputnode.ref_num = 0
>>> nipype_eddycorrect.run() # doctest: +SKIP
Inputs::
inputnode.in_file
inputnode.ref_num
Outputs::
outputnode.eddy_corrected
"""
warnings.warn(
('This workflow is deprecated from v.1.0.0, use '
'nipype.workflows.dmri.preprocess.epi.ecc_pipeline instead'),
DeprecationWarning)
inputnode = pe.Node(niu.IdentityInterface(fields=['in_file', 'ref_num']),
name='inputnode')
pipeline = pe.Workflow(name=name)
split = pe.Node(fsl.Split(dimension='t'), name='split')
pick_ref = pe.Node(niu.Select(), name='pick_ref')
coregistration = pe.MapNode(fsl.FLIRT(no_search=True,
padding_size=1,
interp='trilinear'),
name='coregistration',
iterfield=['in_file'])
merge = pe.Node(fsl.Merge(dimension='t'), name='merge')
outputnode = pe.Node(niu.IdentityInterface(fields=['eddy_corrected']),
name='outputnode')
pipeline.connect([(inputnode, split, [('in_file', 'in_file')]),
(split, pick_ref, [('out_files', 'inlist')]),
(inputnode, pick_ref, [('ref_num', 'index')]),
(split, coregistration, [('out_files', 'in_file')]),
(pick_ref, coregistration, [('out', 'reference')]),
(coregistration, merge, [('out_file', 'in_files')]),
(merge, outputnode, [('merged_file', 'eddy_corrected')])
])
return pipeline
def get_norm_wf(name="norm_wf"):
wf = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['t1w', 't1w_brain']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['t1w_2_MNI_mat', 't1w_2_MNI_warp', 't1w_MNIspace']),
name='outputnode')
# otherwise fnirt is trying to write to the sourcedata dir
t1w_dummy = pe.Node(fsl.ImageMaths(), name="t1w_dummy")
wf.connect(inputnode, "t1w", t1w_dummy, "in_file")
t1w_2_MNI_flirt = pe.Node(fsl.FLIRT(dof=12), name='t1w_2_MNI_flirt')
t1w_2_MNI_flirt.inputs.reference = fsl.Info.standard_image(
'MNI152_T1_1mm_brain.nii.gz')
wf.connect(inputnode, 't1w_brain', t1w_2_MNI_flirt, 'in_file')
wf.connect(t1w_2_MNI_flirt, 'out_matrix_file', outputnode, 't1w_2_MNI_mat')
# 2. CALC. WARP STRUCT -> MNI with FNIRT
# cf. wrt. 2mm
# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=FSL&P=R86108&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
t1w_2_MNI_fnirt = pe.Node(fsl.FNIRT(), name='t1w_2_MNI_fnirt')
t1w_2_MNI_fnirt.inputs.config_file = 'T1_2_MNI152_2mm'
t1w_2_MNI_fnirt.inputs.ref_file = fsl.Info.standard_image(
'MNI152_T1_2mm.nii.gz')
t1w_2_MNI_fnirt.inputs.field_file = True
t1w_2_MNI_fnirt.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(t1w_dummy, 'out_file', t1w_2_MNI_fnirt, 'in_file')
wf.connect(t1w_2_MNI_flirt, 'out_matrix_file', t1w_2_MNI_fnirt,
'affine_file')
wf.connect(t1w_2_MNI_fnirt, 'field_file', outputnode, 't1w_2_MNI_warp')
wf.connect(t1w_2_MNI_fnirt, 'warped_file', outputnode, 't1w_MNIspace')
return wf
def test_nonlinear_register():
from ..registration import create_nonlinear_register
from CPAC.pipeline import nipype_pipeline_engine as pe
import nipype.interfaces.fsl as fsl
## necessary inputs
## -input_brain
## -input_skull
## -reference_brain
## -reference_skull
## -fnirt_config
## -fnirt_warp_res
## input_brain
anat_bet_file = '/home/data/Projects/nuisance_reliability_paper/working_dir_CPAC_order/resting_preproc/anatpreproc/_session_id_NYU_TRT_session1_subject_id_sub05676/anat_skullstrip/mprage_anonymized_RPI_3dT.nii.gz'
## input_skull
## reference_brain
mni_file = '/usr/share/fsl/4.1/data/standard/MNI152_T1_3mm_brain.nii.gz'
## reference_skull
## fnirt_config
fnirt_config = 'T1_2_MNI152_3mm'
## fnirt_warp_res
fnirt_warp_res = None
#?? what is this for?:
func_file = '/home/data/Projects/nuisance_reliability_paper/working_dir_CPAC_order/resting_preproc/nuisance_preproc/_session_id_NYU_TRT_session1_subject_id_sub05676/_csf_threshold_0.4/_gm_threshold_0.2/_wm_threshold_0.66/_run_scrubbing_False/_nc_5/_selector_6.7/regress_nuisance/mapflow/_regress_nuisance0/residual.nii.gz'
mni_workflow = pe.Workflow(name='mni_workflow')
linear_reg = pe.Node(interface=fsl.FLIRT(), name='linear_reg_0')
linear_reg.inputs.cost = 'corratio'
linear_reg.inputs.dof = 6
linear_reg.inputs.interp = 'nearestneighbour'
linear_reg.inputs.in_file = func_file
linear_reg.inputs.reference = anat_bet_file
#T1 to MNI Node
c = create_nonlinear_register()
c.inputs.inputspec.input = anat_bet_file
c.inputs.inputspec.reference = '/usr/share/fsl/4.1/data/standard/MNI152_T1_3mm_brain.nii.gz'
c.inputs.inputspec.fnirt_config = 'T1_2_MNI152_3mm'
#EPI to MNI warp Node
mni_warp = pe.Node(interface=fsl.ApplyWarp(), name='mni_warp')
mni_warp.inputs.ref_file = '/usr/share/fsl/4.1/data/standard/MNI152_T1_3mm_brain.nii.gz'
mni_warp.inputs.in_file = func_file
mni_workflow.connect(c, 'outputspec.nonlinear_xfm', mni_warp, 'field_file')
mni_workflow.connect(linear_reg, 'out_matrix_file', mni_warp, 'premat')
mni_workflow.base_dir = './'
mni_workflow.run()
