def setup_flirt(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = str(tmpdir)
_, infile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
_, reffile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
return (tmp_dir, infile, reffile)
def create_files_in_directory(request):
func_prev_type = set_output_type(request.param)
testdir = os.path.realpath(mkdtemp())
origdir = os.getcwd()
os.chdir(testdir)
filelist = ['a.nii', 'b.nii']
for f in filelist:
hdr = nb.Nifti1Header()
shape = (3, 3, 3, 4)
hdr.set_data_shape(shape)
img = np.random.random(shape)
nb.save(nb.Nifti1Image(img, np.eye(4), hdr),
os.path.join(testdir, f))
out_ext = Info.output_type_to_ext(Info.output_type())
def fin():
if os.path.exists(testdir):
rmtree(testdir)
set_output_type(func_prev_type)
os.chdir(origdir)
request.addfinalizer(fin)
return (filelist, testdir, out_ext)
def setup_infile():
global tmp_infile, tmp_dir
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
file(tmp_infile, 'w')
return tmp_infile, tmp_dir
def setup_infile(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = str(tmpdir)
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
return (tmp_infile, tmp_dir)
def setup_infile():
global tmp_infile, tmp_dir
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, "foo" + ext)
open(tmp_infile, "w")
return tmp_infile, tmp_dir
def setup_flirt(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = str(tmpdir)
_, infile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
_, reffile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
return (tmp_dir, infile, reffile)
def setup_flirt(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
infile = tmpdir.join("infile" + ext)
infile.open("w")
reffile = tmpdir.join("reffile" + ext)
reffile.open("w")
return (tmpdir, infile.strpath, reffile.strpath)
def setup_infile(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = str(tmpdir)
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
return (tmp_infile, tmp_dir)
def setup_flirt(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
infile = tmpdir.join("infile"+ext)
infile.open("w")
reffile = tmpdir.join("reffile"+ext)
reffile.open("w")
return (tmpdir, infile.strpath, reffile.strpath)
def setup_infile():
global tmp_infile, tmp_dir
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
return tmp_infile, tmp_dir
def setup_infile():
global tmp_infile, tmp_dir, cwd
cwd = os.getcwd()
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
file(tmp_infile, 'w')
os.chdir(tmp_dir)
return tmp_infile, tmp_dir
def setup_infile():
global tmp_infile, tmp_dir, cwd
cwd = os.getcwd()
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
os.chdir(tmp_dir)
return tmp_infile, tmp_dir
def setup_infile(request):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
def fin():
shutil.rmtree(tmp_dir)
request.addfinalizer(fin)
return (tmp_infile, tmp_dir)
def setup_flirt(request):
ext = Info.output_type_to_ext(Info.output_type())
tmpdir = tempfile.mkdtemp()
_, infile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
_, reffile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
def teardown_flirt():
shutil.rmtree(tmpdir)
request.addfinalizer(teardown_flirt)
return (tmpdir, infile, reffile)
def setup_flirt(request):
ext = Info.output_type_to_ext(Info.output_type())
tmpdir = tempfile.mkdtemp()
_, infile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
_, reffile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
def teardown_flirt():
shutil.rmtree(tmpdir)
request.addfinalizer(teardown_flirt)
return (tmpdir, infile, reffile)
def setup_infile(request):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
def fin():
shutil.rmtree(tmp_dir)
request.addfinalizer(fin)
return (tmp_infile, tmp_dir)
def create_files_in_directory_plus_output_type(request, tmpdir):
func_prev_type = set_output_type(request.param)
origdir = tmpdir.chdir()
filelist = ['a.nii', 'b.nii']
nifti_image_files(tmpdir.strpath, filelist, shape=(3,3,3,4))
out_ext = Info.output_type_to_ext(Info.output_type())
def fin():
set_output_type(func_prev_type)
origdir.chdir()
request.addfinalizer(fin)
return (filelist, tmpdir.strpath, out_ext)
def create_files_in_directory_plus_output_type(request, tmpdir):
func_prev_type = set_output_type(request.param)
origdir = tmpdir.chdir()
filelist = ['a.nii', 'b.nii']
nifti_image_files(tmpdir.strpath, filelist, shape=(3, 3, 3, 4))
out_ext = Info.output_type_to_ext(Info.output_type())
def fin():
set_output_type(func_prev_type)
origdir.chdir()
request.addfinalizer(fin)
return (filelist, tmpdir.strpath, out_ext)
def create_files_in_directory():
testdir = os.path.realpath(mkdtemp())
origdir = os.getcwd()
os.chdir(testdir)
filelist = ['a.nii', 'b.nii']
for f in filelist:
hdr = nb.Nifti1Header()
shape = (3, 3, 3, 4)
hdr.set_data_shape(shape)
img = np.random.random(shape)
nb.save(nb.Nifti1Image(img, np.eye(4), hdr), os.path.join(testdir, f))
out_ext = Info.output_type_to_ext(Info.output_type())
return filelist, testdir, origdir, out_ext
def run_feat(bold_file, bold_folder, brainmask_file, feat_gen):
from nipype.interfaces.fsl import ImageStats, FEAT, Info
# from bm_functions import gen_default_feat_config
from numpy import shape
from textwrap import dedent
fslFilename = bold_folder + 'feat.fsf'
# Get the number of voxels in the 4D file
statComp = ImageStats()
statComp.inputs.in_file = bold_file
statComp.inputs.op_string = '-v'
numVox = int(statComp.run().outputs.out_stat[0])
# Get the number of raw volumes
statComp.inputs.split_4d = True
numVol = shape(statComp.run().outputs.out_stat)[0]
# Generate the file
standard_T1_brain = Info.standard_image('MNI152_T1_2mm_brain')
theString = feat_gen(bold_folder, bold_file, brainmask_file,
standard_T1_brain, numVox, numVol)
with open(fslFilename, 'w') as out_file:
out_file.write(dedent(theString))
out_file.close()
# Run feat using the previously manipulated config
runFeat = FEAT(fsf_file=fslFilename)
# Run and pass back the foldername
return runFeat.run().outputs.feat_dir
def rs_secondlevel(copes, varcopes, dofs, output_dir, work_dir):
from nipype.workflows.fmri.fsl.estimate import create_fixed_effects_flow
from nipype.interfaces.fsl import Info
level2workflow = pe.Workflow(name="level2workflow")
level2workflow.base_dir = work_dir
fixedfx = create_fixed_effects_flow()
fixedfx.inputs.inputspec.copes = copes
fixedfx.inputs.inputspec.varcopes = varcopes
fixedfx.inputs.inputspec.dof_files = dofs
fixedfx.inputs.l2model.num_copes = len(dofs)
fixedfx.inputs.flameo.mask_file = Info.standard_image(
'MNI152_T1_2mm_brain_mask.nii.gz')
datasink = pe.Node(nio.DataSink(), name='sinker')
datasink.inputs.base_directory = work_dir
level2workflow.connect([(fixedfx, datasink,
[('outputspec.copes', 'copes'),
('outputspec.varcopes', 'varcopes'),
('outputspec.zstats', 'zstats'),
('gendofvolume.dof_volume', 'dofs')])])
level2workflow.run()
#copy data to directory
shutil.rmtree(op.join(work_dir, 'level2workflow'))
files_to_copy = glob(op.join(work_dir, '*', '_flameo0', '*'))
for tmp_fn in files_to_copy:
shutil.copy(tmp_fn, output_dir)
shutil.copy(op.join(work_dir, 'dofs', 'dof_file.nii.gz'), output_dir)
shutil.rmtree(work_dir)
def run_feat(bold_file, bold_folder, brainmask_file, feat_gen):
from nipype.interfaces.fsl import ImageStats, FEAT, Info
# from bm_functions import gen_default_feat_config
from numpy import shape
from textwrap import dedent
fslFilename = bold_folder + 'feat.fsf'
# Get the number of voxels in the 4D file
statComp = ImageStats()
statComp.inputs.in_file = bold_file
statComp.inputs.op_string = '-v'
numVox = int(statComp.run().outputs.out_stat[0])
# Get the number of raw volumes
statComp.inputs.split_4d = True
numVol = shape(statComp.run().outputs.out_stat)[0]
# Generate the file
standard_T1_brain = Info.standard_image('MNI152_T1_2mm_brain')
theString = feat_gen(bold_folder, bold_file, brainmask_file, standard_T1_brain, numVox, numVol)
with open(fslFilename,'w') as out_file:
out_file.write(dedent(theString))
out_file.close()
# Run feat using the previously manipulated config
runFeat = FEAT(fsf_file = fslFilename)
# Run and pass back the foldername
return runFeat.run().outputs.feat_dir
def create_files_in_directory():
testdir = os.path.realpath(mkdtemp())
origdir = os.getcwd()
os.chdir(testdir)
filelist = ['a.nii', 'b.nii']
for f in filelist:
hdr = nb.Nifti1Header()
shape = (3, 3, 3, 4)
hdr.set_data_shape(shape)
img = np.random.random(shape)
nb.save(nb.Nifti1Image(img, np.eye(4), hdr),
os.path.join(testdir, f))
out_ext = Info.output_type_to_ext(Info.output_type())
return filelist, testdir, origdir, out_ext
def set_output_type(fsl_output_type):
prev_output_type = os.environ.get('FSLOUTPUTTYPE', None)
if fsl_output_type is not None:
os.environ['FSLOUTPUTTYPE'] = fsl_output_type
elif 'FSLOUTPUTTYPE' in os.environ:
del os.environ['FSLOUTPUTTYPE']
FSLCommand.set_default_output_type(Info.output_type())
return prev_output_type
def set_output_type(fsl_output_type):
prev_output_type = os.environ.get('FSLOUTPUTTYPE', None)
if fsl_output_type is not None:
os.environ['FSLOUTPUTTYPE'] = fsl_output_type
elif 'FSLOUTPUTTYPE' in os.environ:
del os.environ['FSLOUTPUTTYPE']
FSLCommand.set_default_output_type(Info.output_type())
return prev_output_type
def test_tbss_skeleton(create_files_in_directory):
skeletor = fsl.TractSkeleton()
files, newdir = create_files_in_directory
# Test the underlying command
assert skeletor.cmd == "tbss_skeleton"
# It shouldn't run yet
with pytest.raises(ValueError):
skeletor.run()
# Test the most basic way to use it
skeletor.inputs.in_file = files[0]
# First by implicit argument
skeletor.inputs.skeleton_file = True
assert skeletor.cmdline == "tbss_skeleton -i a.nii -o %s" % os.path.join(
newdir, "a_skeleton.nii")
# Now with a specific name
skeletor.inputs.skeleton_file = "old_boney.nii"
assert skeletor.cmdline == "tbss_skeleton -i a.nii -o old_boney.nii"
# Now test the more complicated usage
bones = fsl.TractSkeleton(in_file="a.nii", project_data=True)
# This should error
with pytest.raises(ValueError):
bones.run()
# But we can set what we need
bones.inputs.threshold = 0.2
bones.inputs.distance_map = "b.nii"
bones.inputs.data_file = "b.nii" # Even though that's silly
# Now we get a command line
assert bones.cmdline == "tbss_skeleton -i a.nii -p 0.200 b.nii %s b.nii %s" % (
Info.standard_image("LowerCingulum_1mm.nii.gz"),
os.path.join(newdir, "b_skeletonised.nii"),
)
# Can we specify a mask?
bones.inputs.use_cingulum_mask = Undefined
bones.inputs.search_mask_file = "a.nii"
assert (bones.cmdline ==
"tbss_skeleton -i a.nii -p 0.200 b.nii a.nii b.nii %s" %
os.path.join(newdir, "b_skeletonised.nii"))
def test_tbss_skeleton():
skeletor = fsl.TractSkeleton()
files, newdir, olddir = create_files_in_directory()
# Test the underlying command
yield assert_equal, skeletor.cmd, "tbss_skeleton"
# It shouldn't run yet
yield assert_raises, ValueError, skeletor.run
# Test the most basic way to use it
skeletor.inputs.in_file = files[0]
# First by implicit argument
skeletor.inputs.skeleton_file = True
yield assert_equal, skeletor.cmdline, \
"tbss_skeleton -i a.nii -o %s"%os.path.join(newdir, "a_skeleton.nii")
# Now with a specific name
skeletor.inputs.skeleton_file = "old_boney.nii"
yield assert_equal, skeletor.cmdline, "tbss_skeleton -i a.nii -o old_boney.nii"
# Now test the more complicated usage
bones = fsl.TractSkeleton(in_file="a.nii", project_data=True)
# This should error
yield assert_raises, ValueError, bones.run
# But we can set what we need
bones.inputs.threshold = 0.2
bones.inputs.distance_map = "b.nii"
bones.inputs.data_file = "b.nii" # Even though that's silly
# Now we get a command line
yield assert_equal, bones.cmdline, \
"tbss_skeleton -i a.nii -p 0.200 b.nii %s b.nii %s"%(Info.standard_image("LowerCingulum_1mm.nii.gz"),
os.path.join(newdir, "b_skeletonised.nii"))
# Can we specify a mask?
bones.inputs.use_cingulum_mask = Undefined
bones.inputs.search_mask_file = "a.nii"
yield assert_equal, bones.cmdline, \
"tbss_skeleton -i a.nii -p 0.200 b.nii a.nii b.nii %s"%os.path.join(newdir, "b_skeletonised.nii")
# Looks good; clean up
clean_directory(newdir, olddir)
def test_registration_workflow(use_FS, use_AFNI_ss):
analysis_info = {
'do_fnirt': False,
'use_FS': use_FS,
'do_FAST': False,
'use_AFNI_ss': use_AFNI_ss
}
wf = create_registration_workflow(analysis_info=analysis_info)
wf.inputs.inputspec.EPI_space_file = op.join(
test_data_path, 'func', 'sub-0020_task-harriri_meanbold.nii.gz')
wf.inputs.inputspec.output_directory = '/tmp/spynoza'
wf.inputs.inputspec.T1_file = op.join(test_data_path, 'anat',
'sub-0020_T1w.nii.gz')
wf.inputs.inputspec.sub_id = 'sub-0020'
wf.inputs.inputspec.standard_file = Info.standard_image(
'MNI152_T1_2mm_brain.nii.gz')
wf.inputs.inputspec.freesurfer_subject_ID = 'sub-0020'
wf.inputs.inputspec.freesurfer_subject_dir = op.join(
op.dirname(test_data_path), 'fs')
wf.base_dir = '/tmp/spynoza/workingdir'
# This is to speed up the analysis
if not analysis_info['use_FS']:
wf = set_parameters_in_nodes(wf,
flirt_e2t={
'interp': 'trilinear',
'cost_func': 'corratio'
},
flirt_t2s={'interp': 'trilinear'})
wf.run()
reg_files = [
'example_func.nii.gz', 'example_func2highres.mat',
'example_func2standard.mat', 'highres.nii.gz',
'highres2example_func.mat', 'highres2standard.mat', 'standard.nii.gz',
'standard2example_func.mat', 'standard2highres.mat'
]
datasink = wf.inputs.inputspec.output_directory = '/tmp/spynoza'
for f in reg_files:
f_path = op.join(datasink, 'sub-0020', 'reg', f)
assert (op.isfile(f_path))
def RENDERPIPE():
#--- 1) Import modules
from nipype.interfaces.ants import Registration, ApplyTransforms
import nipype.pipeline.engine as pe
import matplotlib
import os
from glob import glob
from nilearn import plotting
from nilearn import image
from nipype.interfaces.utility import Function
import nipype.interfaces.fsl.preprocess as fsl
import nipype.interfaces.fsl as fslbase
import nipype.interfaces.fsl.utils as fslu
from nipype.interfaces.fsl import Info
import nipype.interfaces.utility as util
#--- 2) Determine template location and get inputs
template = Info.standard_image('MNI152_T1_2mm_brain.nii.gz')
in_file = raw_input('Please drag in the stats image')
in_matrix_file = raw_input(
'Please drag in the combined registration matrix\n')
transforms = raw_input(
'Please drag in the ANTs normalisation composite transform\n')
thresh = float(raw_input('Please enter the threshold \n'))
#--- 3) Make input node
inputnode = pe.Node(interface=util.IdentityInterface(fields=['thresh']),
name='inputnode')
inputnode.inputs.thresh = thresh
#--- 4) Node for registering to MNI
registerF2S = pe.Node(interface=fsl.ApplyXFM(), name='RENDEREDREG')
registerF2S.inputs.reference = template
registerF2S.inputs.in_file = in_file.strip('\'"')
registerF2S.inputs.in_matrix_file = in_matrix_file.strip('\'"')
NIFTIDIR = os.path.split(registerF2S.inputs.in_file)[0]
#--- 5) Node for ANTs warping to MNI
apply2mean = pe.Node(ApplyTransforms(args='--float',
input_image_type=3,
interpolation='Linear',
invert_transform_flags=[False],
num_threads=1,
reference_image=template,
terminal_output='file'),
name='RENDEREDNORM')
apply2mean.inputs.transforms = transforms.strip('\'"')
#--- 6) Outputnode for warped volume
outputnode = pe.Node(interface=util.IdentityInterface(fields=['warped']),
name='outputnode')
#--- 7) Function for plotting over MNI
def plot(in_file, threshold):
from nilearn import image
from nilearn import plotting
import matplotlib
niftifiledim = len(image.load_img(in_file).shape)
display = plotting.plot_stat_map(stat_map_img=in_file,
black_bg=bool(1),
display_mode='z',
cut_coords=10,
threshold=float(threshold))
matplotlib.pyplot.show()
return niftifiledim
plotter = pe.MapNode(Function(input_names=['in_file', 'threshold'],
output_names='display',
function=plot),
iterfield=['in_file'],
name='PLOTTER')
#--- 8) Define workflow
workflow = pe.Workflow(name='RENDERPIPE')
workflow.base_dir = NIFTIDIR
#--- 9) Connect nodes
workflow.connect(registerF2S, 'out_file', apply2mean, 'input_image')
workflow.connect(apply2mean, 'output_image', outputnode, 'warped')
workflow.connect(outputnode, 'warped', plotter, 'in_file')
workflow.connect(inputnode, 'thresh', plotter, 'threshold')
#--- 10) Run workflow
workflow.write_graph(graph2use='exec')
workflow.run()
def fsl_name(obj, fname):
"""Create valid fsl name, including file extension for output type.
"""
ext = Info.output_type_to_ext(obj.inputs.output_type)
return fname + ext
FSCommand.set_default_subjects_dir(fs_dir)
###
# Specify variables
experiment_dir = '~/nipype_tutorial' # location of experiment folder
input_dir_1st = 'output_fMRI_example_1st' # name of 1st-level output folder
output_dir = 'output_fMRI_example_norm_ants' # name of norm output folder
working_dir = 'workingdir_fMRI_example_norm_ants' # name of norm working directory
subject_list = ['sub001', 'sub002', 'sub003',
'sub004', 'sub005', 'sub006',
'sub007', 'sub008', 'sub009',
'sub010'] # list of subject identifiers
# location of template file
template = Info.standard_image('MNI152_T1_1mm_brain.nii.gz')
###
# Specify Normalization Nodes
# Registration - computes registration between subject's structural and MNI template.
antsreg = Node(Registration(args='--float',
collapse_output_transforms=True,
fixed_image=template,
initial_moving_transform_com=True,
num_threads=1,
output_inverse_warped_image=True,
output_warped_image=True,
sigma_units=['vox']*3,
transforms=['Rigid', 'Affine', 'SyN'],
def fsl_name(obj, fname):
"""Create valid fsl name, including file extension for output type.
"""
ext = Info.output_type_to_ext(obj.inputs.output_type)
return fname + ext
"""Droped from pipeline. Replaced by ApplyTransforms"""
from nipype.interfaces.ants import ComposeMultiTransform
from nipype.interfaces.fsl import Info
compose_transf = ComposeMultiTransform()
compose_transf.inputs.dimension = 3
compose_transf.inputs.reference_image = Info.standard_image('MNI152_T1_1mm.nii.gz')
compose_transf.inputs.transforms = ['transform1InverseWarp.nii.gz', 'transform1Warp.nii.gz']
compose_transf.output_image = 'singletransform.nii.gz'
`
from nipype.pipeline.engine import Workflow, Node, MapNode
from nipype.interfaces.fsl import Info
# FreeSurfer - Specify the location of the freesurfer folder
fs_dir = '/data/adamt/Apps/fs6beta'
FSCommand.set_default_subjects_dir(fs_dir)
# Specify variables
experiment_dir = '/data/Hippo_hr/cpb/' # location of experiment folder
input_dir_1st = 'output_ANTS_test_1st_lvl' # name of 1st-level output folder
output_dir = 'output_ANTS_test_norm' # name of norm output folder
working_dir = '/home/zhoud4/Hippo_hr/cpb/ants1/lhipp3_batch/' # name of norm working directory
subject_list = ['d701', 'd702', 'd703'] # list of subject identifiers
# location of template file
template = Info.standard_image('.nii.gz')
# Registration (good) - computes registration between subject's structural and MNI template.
antsreg = Node(Registration(args='--float',
collapse_output_transforms=True,
fixed_image=template,
initial_moving_transform_com=True,
num_threads=1,
output_inverse_warped_image=True,
output_warped_image=True,
sigma_units=['vox']*3,
transforms=['Rigid', 'Affine', 'SyN'],
terminal_output='file',
winsorize_lower_quantile=0.005,
winsorize_upper_quantile=0.995,
convergence_threshold=[1e-06],
def setup_infile(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_infile = tmpdir.join('foo' + ext)
tmp_infile.open("w")
return (tmp_infile.strpath, tmpdir.strpath)
def custom_level1design_feat(func_file,
highres_file=None,
session_info=None,
output_dirname='firstlevel',
contrasts='single-trial',
smoothing=0,
temp_deriv=False,
registration='full',
highpass=100,
slicetiming=None,
motion_correction=None,
bet=True,
prewhitening=True,
motion_regression=None,
thresholding='uncorrected',
p_val=0.05,
z_val=2.3,
mask=None,
hrf='doublegamma',
open_feat_html=False):
""" Custom implementation of a FSL create-level1-design function.
This function (which can be wrapped in a custom Nipype Function node) creates an FSL design.fsf
file. This function is similar to the Nipype Level1Design node (interfaces.fsl.model) but allows
for way more options to be set.
Parameters
----------
func_file : str
Path to functional file (4D) with timeseries data
highres_file : str
Path to file corresponding to high-resolution anatomical scan (should already be skull-stripped!).
Only necessary if doing functional-highres-standard registration (i.e. registration = 'full');
otherwise, set to None.
session_info : Nipype Bunch-object
Bunch-object (dict-like) with information about stimulus-related and nuisance regressors.
output_dirname : str
Name of output directory (.feat will be appended to it).
contrasts : str, tuple, or list
(List of) tuple(s) with defined contrasts. Should be formatted using the Nipype syntax:
`(name_of_contrast, 'T', [cond_name_1, cond_name_2], [weight_1, weight_2])` for a t-contrast,
or `(name_of_f_test, 'F', [contrast_1, contrast_2])` for F-tests.
smoothing : float or int
Smoothing kernel in FWHM (mm)
temp_deriv : bool
Whether to include temporal derivates of real EVs.
registration : str
Registration-scheme to apply. Currently supports three types: 'full', which registers
the functional file to the high-res anatomical (using FLIRT BBR) and subsequent linear-
non-linear registration to the MNI152 (2mm) standard brain (using FNIRT); another option
is 'fmriprep', which only calculates a 3-parameter (translation only) transformation because
output from the fmriprep-preprocessing-pipeline is already registered to MNI but is still in
native dimensions (i.e. EPI-space). Last option is 'none', which doesn't do any registration.
highpass : int
Length (in seconds) of FSL highpass filter to apply.
slicetiming : str
Whether to apply slice-time correction; options are 'up' (ascending), 'down' (descending),
or 'no' (no slicetiming correction).
motion_correction : bool
Whether to apply motion-correction (MCFLIRT).
bet : bool
Whether to BET (skullstrip) the functional file.
prewhitening : bool
Whether to do prewhitening.
motion_regression : str
Whether to do motion-regression. Options: 'no' (no motion regression), 'yes' (standard 6 parameters motion
regression), 'ext' (extended 24 parameter motion regression).
thresholding : str
What type of thresholding to apply. Options: 'none', 'uncorrected', 'voxel', 'cluster'.
p_val : float
What p-value to use in thresholding.
z_val : float
What minimum z-value to use in cluster-correction
mask : str
File to use in pre-thresholding masking. Setting to None means no masking.
hrf : str
What HRF-model to use. Default is 'doublegamma', but other options are: 'gamma',
'gammabasisfunctions', 'gaussian'.
open_feat_html : bool
Whether to automatically open HTML-progress report.
Returns
-------
design_file : str
The path to the created design.fsf file
confound_txt_file : str
Path to the created confounds.txt file
ev_files : list
List with paths to EV-text-files.
"""
import os.path as op
import nibabel as nib
from nipype.interfaces.fsl import Info
import numpy as np
import spynoza
if isinstance(session_info, list):
if len(session_info) == 1:
session_info = session_info[0]
if registration == 'full' and highres_file is None:
raise ValueError(
"If you want to do a full registration, you need to specify a highres file!"
)
if motion_correction in (0, False,
'yes') and motion_regression in ('yes', True, 1,
'ext', 2):
raise ValueError(
"If you want to do motion-regression, make sure to turn on motion-correction!"
)
if hrf == 'gammabasisfunctions' and temp_deriv:
print(
"Cannot add temporal deriv when hrf = gammabasisfunctions; setting temp-deriv to False"
)
temp_deriv = False
n_orig_evs = len(session_info.conditions)
if contrasts == 'single-trial':
cons = []
for i in range(n_orig_evs):
con_values = np.zeros(len(session_info.conditions))
con_values[i] = 1
this_con = (session_info.conditions[i], 'T',
session_info.conditions, con_values)
cons.append(this_con)
f_con = ('f_all', 'F', cons)
cons.append(f_con)
contrasts = cons
elif isinstance(contrasts, list): # assume nipype style contrasts
for i, con in enumerate(contrasts):
weights = np.zeros(n_orig_evs)
this_i = 0
for ii, ev in enumerate(session_info.conditions):
for iii, this_entry in enumerate(con[2]):
if ev == this_entry:
weights[ii] = con[3][iii]
contrasts[i] = (con[0], con[1], con[2], weights.tolist())
t_contrasts = [con for con in contrasts if con[1] == 'T']
f_contrasts = [con for con in contrasts if con[1] == 'F']
n_con = len(t_contrasts)
n_ftest = len(f_contrasts)
n_real_evs = n_orig_evs
if temp_deriv:
n_real_evs *= 2
elif hrf == 'gammabasisfunctions':
n_real_evs *= 3 # ToDo: allow more than 3 basis funcs
if temp_deriv:
con_mode_old = 'real'
con_mode = 'real'
else:
con_mode_old = 'orig'
con_mode = 'orig'
arg_dict = dict(
temp_deriv={
True: 1,
1: 1,
False: 0,
0: 0
},
slicetiming={
'no': 0,
0: 0,
None: 0,
'up': 1,
1: 1,
'down': 2,
2: 2
},
motion_correction={
True: 1,
1: 1,
False: 0,
0: 0,
None: 0
},
bet={
True: 1,
1: 1,
False: 0,
0: 0,
None: 0
},
motion_regression={
'no': 0,
False: 0,
None: 0,
'yes': 1,
True: 1,
1: 1,
'ext': 2,
2: 2
},
thresholding={
'none': 0,
None: 0,
'no': 0,
0: 0,
'uncorrected': 1,
'Uncorrected': 1,
1: 1,
'voxel': 2,
'Voxel': 2,
2: 2,
'cluster': 3,
'Cluster': 3,
3: 3
},
prewhitening={
True: 1,
1: 1,
False: 0,
None: 0,
0: 0
},
hrf={
'doublegamma': 3,
'none': 0,
None: 0,
'gaussian': 1,
'gamma': 2,
'gammabasisfunctions': 4
}, #,
#'sinebasisfunctions': 5,
#'firbasisfunctions': 6},
open_feat_html={
True: 1,
1: 1,
False: 0,
0: 0,
None: 0
})
reg_dict = {
'full': {
'reghighres_yn': 1,
'reghighres_dof': 'BBR',
'regstandard_yn': 1,
'regstandard': Info.standard_image('MNI152_T1_2mm_brain.nii.gz'),
'regstandard_dof': 12,
'regstandard_nonlinear_yn': 1
},
'none': {
'reghighres_yn': 0,
'regstandard_yn': 0
},
'fmriprep': {
'reghighres_yn': 0,
'regstandard_yn': 1,
'regstandard_dof': 3,
'regstandard_nonlinear_yn': 0
}
}
data_dir = op.join(op.dirname(spynoza.__file__), 'data')
fsf_template = op.join(data_dir, 'fsf_templates',
'firstlevel_template.fsf')
with open(fsf_template, 'r') as f:
fsf_template = f.readlines()
fsf_template = [
txt.replace('\n', '') for txt in fsf_template if txt != '\n'
]
fsf_template = [txt for txt in fsf_template
if txt[0] != '#'] # remove commnts
hdr = nib.load(func_file).header
args = {
'outputdir': "\"%s\"" % output_dirname,
'tr': hdr['pixdim'][4],
'npts': hdr['dim'][4],
'smooth': smoothing,
'deriv_yn': arg_dict['temp_deriv'][temp_deriv],
'temphp_yn': 1 if highpass else 0,
'paradigm_hp': highpass,
'st': arg_dict['slicetiming'][slicetiming],
'mc': arg_dict['motion_correction'][motion_correction],
'bet_yn': arg_dict['bet'][bet],
'prewhiten_yn': arg_dict['prewhitening'][prewhitening],
'motionevs': arg_dict['motion_regression'][motion_regression],
'threshmask': mask if mask is not None else "",
'thresh': arg_dict['thresholding'][thresholding],
'prob_thresh': p_val,
'z_thresh': z_val,
'evs_orig': n_orig_evs,
'evs_real': n_real_evs,
'ncon_orig': n_con,
'ncon_real': n_con,
'nftests_orig': n_ftest,
'nftests_real': n_ftest,
'con_mode_old': con_mode_old,
'con_mode': con_mode,
'featwatcher_yn': arg_dict['open_feat_html'][open_feat_html],
'confoundevs': 1
}
args.update(reg_dict[registration])
fsf_out = []
# 4D AVW data or FEAT directory (1)
fsf_out.append("set feat_files(1) \"%s\"" % func_file)
confound_txt_file = op.join(op.abspath('confounds.txt'))
if hasattr(session_info, 'regressors'):
confounds = np.array(session_info.regressors).T
np.savetxt(confound_txt_file,
confounds,
fmt=str('%.5f'),
delimiter='\t')
fsf_out.append('set confoundev_files(1) \"%s\"' % confound_txt_file)
else:
open(confound_txt_file, 'a').close() # for compatibility issues
fsf_out.append('set confoundev_files(1) \"\"')
if highres_file is not None:
fsf_template.append("set highres_files(1) \"%s\"" % highres_file)
for line in fsf_template:
if any(key in line for key in args.keys()):
parts = [str(txt) for txt in line.split(' ') if txt]
for key, value in args.items():
if 'set fmri(%s)' % key in line:
parts[-1] = str(value)
break
fsf_out.append(" ".join(parts))
else:
fsf_out.append(line)
ev_files = []
for i in range(n_orig_evs):
fname = op.join(op.abspath(session_info.conditions[i] + '.txt'))
info = np.vstack((session_info.onsets[i], session_info.durations[i],
session_info.amplitudes[i])).T
ev_files.append(fname)
np.savetxt(fname, info, fmt=str('%.3f'), delimiter='\t')
fsf_out.append('set fmri(evtitle%i) \"%s\"' %
((i + 1), session_info.conditions[i]))
fsf_out.append('set fmri(shape%i) 3' % (i + 1))
fsf_out.append('set fmri(convolve%i) %i' %
((i + 1), arg_dict['hrf'][hrf]))
fsf_out.append('set fmri(convolve_phase%i) 0' % (i + 1))
# Only relevant if hrf = 'gamma'
fsf_out.append('set fmri(gammasigma%i) 3' % (i + 1))
fsf_out.append('set fmri(gammadelay%i) 6' % (i + 1))
# Only relevant if hrf = 'gammabasisfunctions'
fsf_out.append('set fmri(basisfnum%i) 3' % (i + 1))
fsf_out.append('set fmri(basisfwidth%i) 15' % (i + 1))
fsf_out.append('set fmri(basisorth%i) 0' % (i + 1))
fsf_out.append('set fmri(tempfilt_yn%i) %i' %
((i + 1), args['temphp_yn']))
fsf_out.append('set fmri(deriv_yn%i) %i' % ((i + 1), args['deriv_yn']))
fsf_out.append('set fmri(custom%i) %s' % ((i + 1), fname))
for x in range(n_orig_evs + 1):
fsf_out.append('set fmri(ortho%i.%i) 0' % ((i + 1), x))
if contrasts and contrasts is not None:
for i, contrast in enumerate(t_contrasts):
cname, ctype, ccond, cweights = contrast
fsf_out.append('set fmri(conpic_real.%i) 1' % (i + 1))
fsf_out.append('set fmri(conname_real.%i) \"%s\"' %
((i + 1), cname))
fsf_out.append('set fmri(conpic_orig.%i) 1' % (i + 1))
fsf_out.append('set fmri(conname_orig.%i) \"%s\"' %
((i + 1), cname))
for ii, weight in enumerate(cweights):
fsf_out.append('set fmri(con_orig%i.%i) %.1f' %
(i + 1, ii + 1, float(weight)))
ratio_orig_real = int(n_real_evs / n_orig_evs)
real_weights = [[w] + [0] * (ratio_orig_real - 1)
for w in cweights]
real_weights = [
item for sublist in real_weights for item in sublist
]
for ii, weight in enumerate(real_weights):
fsf_out.append('set fmri(con_real%i.%i) %.1f' %
(i + 1, ii + 1, float(weight)))
for i, contrast in enumerate(f_contrasts):
for ii, tcon in enumerate(t_contrasts):
to_set = 1 if tcon in contrast[2] else 0
fsf_out.append('set fmri(ftest_orig%i.%i) %i' %
(i + 1, ii + 1, to_set))
fsf_out.append('set fmri(ftest_real%i.%i) %i' %
(i + 1, ii + 1, to_set))
design_file = op.join(op.abspath('design.fsf'))
with open(design_file, 'w') as fsfout:
print("Writing fsf to %s" % design_file)
fsfout.write("\n".join(fsf_out))
return design_file, confound_txt_file, ev_files
import os
from pathlib import Path
from datetime import datetime as dt
import pytest
from templateflow.api import get as get_template
from nipype.interfaces.fsl import Info as FSLInfo
from nipype.interfaces.freesurfer import Info as FreeSurferInfo
filepath = os.path.dirname(os.path.realpath(__file__))
datadir = os.path.realpath(os.path.join(filepath, 'data'))
test_data_env = os.getenv('TEST_DATA_HOME',
str(Path.home() / '.cache' / 'stanford-crn'))
data_dir = Path(test_data_env) / 'ds003_downsampled'
has_fsl = FSLInfo.version() is not None
has_freesurfer = FreeSurferInfo.version() is not None
def _run_interface_mock(objekt, runtime):
runtime.returncode = 0
runtime.endTime = dt.isoformat(dt.utcnow())
objekt._out_report = os.path.abspath(objekt.inputs.out_report)
objekt._post_run_hook(runtime)
objekt._generate_report()
return runtime
@pytest.fixture
def reference():
def setup_infile(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_infile = tmpdir.join('foo' + ext)
tmp_infile.open("w")
return (tmp_infile.strpath, tmpdir.strpath)
fs_dir = '~/nipype_tutorial/freesurfer'
FSCommand.set_default_subjects_dir(fs_dir)
###
# Specify variables
experiment_dir = '~/nipype_tutorial' # location of experiment folder
input_dir_1st = 'output_fMRI_example_1st' # name of 1st-level output folder
output_dir = 'output_fMRI_example_norm_ants' # name of norm output folder
working_dir = 'workingdir_fMRI_example_norm_ants' # name of norm working directory
subject_list = [
'sub001', 'sub002', 'sub003', 'sub004', 'sub005', 'sub006', 'sub007',
'sub008', 'sub009', 'sub010'
] # list of subject identifiers
# location of template file
template = Info.standard_image('MNI152_T1_1mm_brain.nii.gz')
###
# Specify Normalization Nodes
# Registration - computes registration between subject's structural and MNI template.
antsreg = Node(Registration(args='--float',
collapse_output_transforms=True,
fixed_image=template,
initial_moving_transform_com=True,
num_threads=1,
output_inverse_warped_image=True,
output_warped_image=True,
sigma_units=['vox'] * 3,
transforms=['Rigid', 'Affine', 'SyN'],
terminal_output='file',
def rs_grouplevel(copes, varcopes, dofs, output_dir, work_dir):
from nipype.interfaces.fsl.model import MultipleRegressDesign
from nipype.interfaces.utility import Function
from nipype.interfaces.fsl.model import FLAMEO
from nipype.interfaces.fsl.model import SmoothEstimate
from connectivity.interfaces import Cluster
from nipype.interfaces.fsl.utils import Merge
from nipype.interfaces.fsl import Info
from connectivity.interfaces import PtoZ
grplevelworkflow = pe.Workflow(name="grplevelworkflow")
grplevelworkflow.base_dir = work_dir
merger = Merge()
merger.inputs.dimension = 't'
merger.inputs.in_files = copes
merger.inputs.merged_file = op.join(work_dir, 'cope.nii.gz')
merger.run()
merger.inputs.in_files = varcopes
merger.inputs.merged_file = op.join(work_dir, 'varcope.nii.gz')
merger.run()
merger.inputs.in_files = dofs
merger.inputs.merged_file = op.join(work_dir, 'dof.nii.gz')
merger.run()
model = pe.Node(interface=MultipleRegressDesign(), name='model')
model.inputs.contrasts = [['mean', 'T', ['roi'], [1]]]
model.inputs.regressors = dict(roi=np.ones(len(copes)).tolist())
flameo = pe.Node(interface=FLAMEO(), name='flameo')
flameo.inputs.cope_file = op.join(work_dir, 'cope.nii.gz')
flameo.inputs.var_cope_file = op.join(work_dir, 'varcope.nii.gz')
flameo.inputs.dof_var_cope_file = op.join(work_dir, 'dof.nii.gz')
flameo.inputs.run_mode = 'flame1'
flameo.inputs.mask_file = Info.standard_image(
'MNI152_T1_2mm_brain_mask.nii.gz')
grplevelworkflow.connect(model, 'design_con', flameo, 't_con_file')
grplevelworkflow.connect(model, 'design_grp', flameo, 'cov_split_file')
grplevelworkflow.connect(model, 'design_mat', flameo, 'design_file')
smoothest = pe.Node(SmoothEstimate(), name='smooth_estimate')
grplevelworkflow.connect(flameo, 'zstats', smoothest, 'residual_fit_file')
smoothest.inputs.mask_file = Info.standard_image(
'MNI152_T1_2mm_brain_mask.nii.gz')
smoothest.inputs.dof = len(dofs) - 1
cluster = pe.Node(Cluster(), name='cluster')
ptoz = pe.Node(PtoZ(), name='ptoz')
ptoz.inputs.pvalue = 0.001
calculate_resels = pe.Node(Function(input_names=["volume", "resels"],
output_names=["resels"],
function=calcres),
name="calcres")
grplevelworkflow.connect(smoothest, 'resels', cluster, 'resels')
grplevelworkflow.connect(smoothest, 'resels', calculate_resels, 'resels')
grplevelworkflow.connect(smoothest, 'volume', calculate_resels, 'volume')
grplevelworkflow.connect(calculate_resels, 'resels', ptoz, 'resels')
grplevelworkflow.connect(ptoz, 'zstat', cluster, 'threshold')
cluster.inputs.connectivity = 26
cluster.inputs.out_threshold_file = True
cluster.inputs.out_index_file = True
cluster.inputs.out_localmax_txt_file = True
cluster.inputs.voxthresh = True
grplevelworkflow.connect(flameo, 'zstats', cluster, 'in_file')
datasink = pe.Node(nio.DataSink(), name='sinker')
datasink.inputs.base_directory = work_dir
grplevelworkflow.connect(flameo, 'zstats', datasink, 'z')
grplevelworkflow.connect(cluster, 'threshold_file', datasink, 'z_thresh')
grplevelworkflow.run()
shutil.rmtree(op.join(work_dir, 'grplevelworkflow'))
#copy data to directory
shutil.copyfile(op.join(work_dir, 'z', 'zstat1.nii.gz'),
op.join(output_dir, 'z.nii.gz'))
shutil.copyfile(op.join(work_dir, 'z_thresh', 'zstat1_threshold.nii.gz'),
op.join(output_dir, 'z_level-voxel_corr-FWE.nii.gz'))
shutil.rmtree(work_dir)
def custom_level1design_feat(func_file, highres_file=None, session_info=None, output_dirname='firstlevel',
contrasts='single-trial', smoothing=0, temp_deriv=False, registration='full', highpass=100,
slicetiming=None, motion_correction=None, bet=True, prewhitening=True, motion_regression=None,
thresholding='uncorrected', p_val=0.05, z_val=2.3, mask=None, hrf='doublegamma',
open_feat_html=False):
""" Custom implementation of a FSL create-level1-design function.
This function (which can be wrapped in a custom Nipype Function node) creates an FSL design.fsf
file. This function is similar to the Nipype Level1Design node (interfaces.fsl.model) but allows
for way more options to be set.
Parameters
----------
func_file : str
Path to functional file (4D) with timeseries data
highres_file : str
Path to file corresponding to high-resolution anatomical scan (should already be skull-stripped!).
Only necessary if doing functional-highres-standard registration (i.e. registration = 'full');
otherwise, set to None.
session_info : Nipype Bunch-object
Bunch-object (dict-like) with information about stimulus-related and nuisance regressors.
output_dirname : str
Name of output directory (.feat will be appended to it).
contrasts : str, tuple, or list
(List of) tuple(s) with defined contrasts. Should be formatted using the Nipype syntax:
`(name_of_contrast, 'T', [cond_name_1, cond_name_2], [weight_1, weight_2])` for a t-contrast,
or `(name_of_f_test, 'F', [contrast_1, contrast_2])` for F-tests.
smoothing : float or int
Smoothing kernel in FWHM (mm)
temp_deriv : bool
Whether to include temporal derivates of real EVs.
registration : str
Registration-scheme to apply. Currently supports three types: 'full', which registers
the functional file to the high-res anatomical (using FLIRT BBR) and subsequent linear-
non-linear registration to the MNI152 (2mm) standard brain (using FNIRT); another option
is 'fmriprep', which only calculates a 3-parameter (translation only) transformation because
output from the fmriprep-preprocessing-pipeline is already registered to MNI but is still in
native dimensions (i.e. EPI-space). Last option is 'none', which doesn't do any registration.
highpass : int
Length (in seconds) of FSL highpass filter to apply.
slicetiming : str
Whether to apply slice-time correction; options are 'up' (ascending), 'down' (descending),
or 'no' (no slicetiming correction).
motion_correction : bool
Whether to apply motion-correction (MCFLIRT).
bet : bool
Whether to BET (skullstrip) the functional file.
prewhitening : bool
Whether to do prewhitening.
motion_regression : str
Whether to do motion-regression. Options: 'no' (no motion regression), 'yes' (standard 6 parameters motion
regression), 'ext' (extended 24 parameter motion regression).
thresholding : str
What type of thresholding to apply. Options: 'none', 'uncorrected', 'voxel', 'cluster'.
p_val : float
What p-value to use in thresholding.
z_val : float
What minimum z-value to use in cluster-correction
mask : str
File to use in pre-thresholding masking. Setting to None means no masking.
hrf : str
What HRF-model to use. Default is 'doublegamma', but other options are: 'gamma',
'gammabasisfunctions', 'gaussian'.
open_feat_html : bool
Whether to automatically open HTML-progress report.
Returns
-------
design_file : str
The path to the created design.fsf file
confound_txt_file : str
Path to the created confounds.txt file
ev_files : list
List with paths to EV-text-files.
"""
import os.path as op
import nibabel as nib
from nipype.interfaces.fsl import Info
import numpy as np
import spynoza
if isinstance(session_info, list):
if len(session_info) == 1:
session_info = session_info[0]
if registration == 'full' and highres_file is None:
raise ValueError("If you want to do a full registration, you need to specify a highres file!")
if motion_correction in (0, False, 'yes') and motion_regression in ('yes', True, 1, 'ext', 2):
raise ValueError("If you want to do motion-regression, make sure to turn on motion-correction!")
if hrf == 'gammabasisfunctions' and temp_deriv:
print("Cannot add temporal deriv when hrf = gammabasisfunctions; setting temp-deriv to False")
temp_deriv = False
n_orig_evs = len(session_info.conditions)
if contrasts == 'single-trial':
cons = []
for i in range(n_orig_evs):
con_values = np.zeros(len(session_info.conditions))
con_values[i] = 1
this_con = (session_info.conditions[i], 'T', session_info.conditions, con_values)
cons.append(this_con)
f_con = ('f_all', 'F', cons)
cons.append(f_con)
contrasts = cons
elif isinstance(contrasts, list): # assume nipype style contrasts
for i, con in enumerate(contrasts):
weights = np.zeros(n_orig_evs)
this_i = 0
for ii, ev in enumerate(session_info.conditions):
for iii, this_entry in enumerate(con[2]):
if ev == this_entry:
weights[ii] = con[3][iii]
contrasts[i] = (con[0], con[1], con[2], weights.tolist())
t_contrasts = [con for con in contrasts if con[1] == 'T']
f_contrasts = [con for con in contrasts if con[1] == 'F']
n_con = len(t_contrasts)
n_ftest = len(f_contrasts)
n_real_evs = n_orig_evs
if temp_deriv:
n_real_evs *= 2
elif hrf == 'gammabasisfunctions':
n_real_evs *= 3 # ToDo: allow more than 3 basis funcs
if temp_deriv:
con_mode_old = 'real'
con_mode = 'real'
else:
con_mode_old = 'orig'
con_mode = 'orig'
arg_dict = dict(temp_deriv={True: 1, 1: 1, False: 0, 0: 0},
slicetiming={'no': 0, 0: 0, None: 0,
'up': 1, 1: 1,
'down': 2, 2: 2},
motion_correction={True: 1, 1: 1, False: 0, 0: 0, None: 0},
bet={True: 1, 1: 1, False: 0, 0: 0, None: 0},
motion_regression={'no': 0, False: 0, None: 0,
'yes': 1, True: 1, 1: 1,
'ext': 2, 2: 2},
thresholding={'none': 0, None: 0, 'no': 0, 0: 0,
'uncorrected': 1, 'Uncorrected': 1, 1: 1,
'voxel': 2, 'Voxel': 2, 2: 2,
'cluster': 3, 'Cluster': 3, 3: 3},
prewhitening={True: 1, 1: 1, False: 0, None: 0, 0: 0},
hrf={'doublegamma': 3,
'none': 0, None: 0,
'gaussian': 1,
'gamma': 2,
'gammabasisfunctions': 4}, #,
#'sinebasisfunctions': 5,
#'firbasisfunctions': 6},
open_feat_html={True: 1, 1: 1,
False: 0, 0: 0, None: 0}
)
reg_dict = {'full': {'reghighres_yn': 1,
'reghighres_dof': 'BBR',
'regstandard_yn': 1,
'regstandard': Info.standard_image('MNI152_T1_2mm_brain.nii.gz'),
'regstandard_dof': 12,
'regstandard_nonlinear_yn': 1},
'none': {'reghighres_yn': 0,
'regstandard_yn': 0},
'fmriprep': {'reghighres_yn': 0,
'regstandard_yn': 1,
'regstandard_dof': 3,
'regstandard_nonlinear_yn': 0}
}
data_dir = op.join(op.dirname(spynoza.__file__), 'data')
fsf_template = op.join(data_dir, 'fsf_templates', 'firstlevel_template.fsf')
with open(fsf_template, 'r') as f:
fsf_template = f.readlines()
fsf_template = [txt.replace('\n', '') for txt in fsf_template if txt != '\n']
fsf_template = [txt for txt in fsf_template if txt[0] != '#'] # remove commnts
hdr = nib.load(func_file).header
args = {'outputdir': "\"%s\"" % output_dirname,
'tr': hdr['pixdim'][4],
'npts': hdr['dim'][4],
'smooth': smoothing,
'deriv_yn': arg_dict['temp_deriv'][temp_deriv],
'temphp_yn': 1 if highpass else 0,
'paradigm_hp': highpass,
'st': arg_dict['slicetiming'][slicetiming],
'mc': arg_dict['motion_correction'][motion_correction],
'bet_yn': arg_dict['bet'][bet],
'prewhiten_yn': arg_dict['prewhitening'][prewhitening],
'motionevs': arg_dict['motion_regression'][motion_regression],
'threshmask': mask if mask is not None else "",
'thresh': arg_dict['thresholding'][thresholding],
'prob_thresh': p_val,
'z_thresh': z_val,
'evs_orig': n_orig_evs,
'evs_real': n_real_evs,
'ncon_orig': n_con,
'ncon_real': n_con,
'nftests_orig': n_ftest,
'nftests_real': n_ftest,
'con_mode_old': con_mode_old,
'con_mode': con_mode,
'featwatcher_yn': arg_dict['open_feat_html'][open_feat_html],
'confoundevs': 1}
args.update(reg_dict[registration])
fsf_out = []
# 4D AVW data or FEAT directory (1)
fsf_out.append("set feat_files(1) \"%s\"" % func_file)
confound_txt_file = op.join(op.abspath('confounds.txt'))
if hasattr(session_info, 'regressors'):
confounds = np.array(session_info.regressors).T
np.savetxt(confound_txt_file, confounds, fmt=str('%.5f'), delimiter='\t')
fsf_out.append('set confoundev_files(1) \"%s\"' % confound_txt_file)
else:
open(confound_txt_file, 'a').close() # for compatibility issues
fsf_out.append('set confoundev_files(1) \"\"')
if highres_file is not None:
fsf_template.append("set highres_files(1) \"%s\"" % highres_file)
for line in fsf_template:
if any(key in line for key in args.keys()):
parts = [str(txt) for txt in line.split(' ') if txt]
for key, value in args.items():
if 'set fmri(%s)' % key in line:
parts[-1] = str(value)
break
fsf_out.append(" ".join(parts))
else:
fsf_out.append(line)
ev_files = []
for i in range(n_orig_evs):
fname = op.join(op.abspath(session_info.conditions[i] + '.txt'))
info = np.vstack((session_info.onsets[i],
session_info.durations[i],
session_info.amplitudes[i])).T
ev_files.append(fname)
np.savetxt(fname, info, fmt=str('%.3f'), delimiter='\t')
fsf_out.append('set fmri(evtitle%i) \"%s\"' % ((i + 1), session_info.conditions[i]))
fsf_out.append('set fmri(shape%i) 3' % (i + 1))
fsf_out.append('set fmri(convolve%i) %i' % ((i + 1), arg_dict['hrf'][hrf]))
fsf_out.append('set fmri(convolve_phase%i) 0' % (i + 1))
# Only relevant if hrf = 'gamma'
fsf_out.append('set fmri(gammasigma%i) 3' % (i + 1))
fsf_out.append('set fmri(gammadelay%i) 6' % (i + 1))
# Only relevant if hrf = 'gammabasisfunctions'
fsf_out.append('set fmri(basisfnum%i) 3' % (i + 1))
fsf_out.append('set fmri(basisfwidth%i) 15' % (i + 1))
fsf_out.append('set fmri(basisorth%i) 0' % (i + 1))
fsf_out.append('set fmri(tempfilt_yn%i) %i' % ((i + 1), args['temphp_yn']))
fsf_out.append('set fmri(deriv_yn%i) %i' % ((i + 1), args['deriv_yn']))
fsf_out.append('set fmri(custom%i) %s' % ((i + 1), fname))
for x in range(n_orig_evs + 1):
fsf_out.append('set fmri(ortho%i.%i) 0' % ((i + 1), x))
if contrasts and contrasts is not None:
for i, contrast in enumerate(t_contrasts):
cname, ctype, ccond, cweights = contrast
fsf_out.append('set fmri(conpic_real.%i) 1' % (i + 1))
fsf_out.append('set fmri(conname_real.%i) \"%s\"' % ((i + 1),
cname))
fsf_out.append('set fmri(conpic_orig.%i) 1' % (i + 1))
fsf_out.append('set fmri(conname_orig.%i) \"%s\"' % ((i + 1),
cname))
for ii, weight in enumerate(cweights):
fsf_out.append('set fmri(con_orig%i.%i) %.1f' % (i + 1, ii + 1, float(weight)))
ratio_orig_real = int(n_real_evs / n_orig_evs)
real_weights = [[w] + [0] * (ratio_orig_real - 1) for w in cweights]
real_weights = [item for sublist in real_weights for item in sublist]
for ii, weight in enumerate(real_weights):
fsf_out.append('set fmri(con_real%i.%i) %.1f' % (i + 1, ii + 1, float(weight)))
for i, contrast in enumerate(f_contrasts):
for ii, tcon in enumerate(t_contrasts):
to_set = 1 if tcon in contrast[2] else 0
fsf_out.append('set fmri(ftest_orig%i.%i) %i' % (i + 1, ii + 1, to_set))
fsf_out.append('set fmri(ftest_real%i.%i) %i' % (i + 1, ii + 1, to_set))
design_file = op.join(op.abspath('design.fsf'))
with open(design_file, 'w') as fsfout:
print("Writing fsf to %s" % design_file)
fsfout.write("\n".join(fsf_out))
return design_file, confound_txt_file, ev_files
def NORMPIPE():
#--- 1) Import modules
from nipype.interfaces.ants import Registration, ApplyTransforms
import nipype.pipeline.engine as pe
import matplotlib
import os
from glob import glob
from nilearn import plotting
from nilearn import image
from nipype.interfaces.utility import Function
import nipype.interfaces.fsl.preprocess as fsl
import nipype.interfaces.fsl as fslbase
import nipype.interfaces.fsl.utils as fslu
from nipype.interfaces.fsl import Info
import nipype.interfaces.utility as util
INITDIR = os.getcwd()
#--- 2) Define input node
template = Info.standard_image('MNI152_T1_2mm_brain.nii.gz')
inputnode = pe.Node(interface=util.IdentityInterface(fields=['standard']),
name='inputspec')
inputnode.inputs.standard = template
#--- 3) Get inputs and define node for registering EPI to structural.
alsonorm = bool(input('Also normalise?\n'))
epireg = pe.Node(interface=fslbase.EpiReg(), name='EPIREG')
t1_brain = raw_input(
'Please drag in the brain-extracted structural volume\n')
t1_head = raw_input(
'Please drag in the non-brain extracted structural volume\n')
epi = raw_input('Please drag in the mean functional volume.\n')
epireg.inputs.t1_brain = t1_brain.strip('\'"')
epireg.inputs.t1_head = t1_head.strip('\'"')
epireg.inputs.epi = epi.strip('\'"')
NIFTIDIR = os.path.split(epireg.inputs.t1_brain)[0]
#--- 4) Register the T1 to the MNI
registerT12S = pe.Node(interface=fsl.FLIRT(), name='REGISTEREDT12MNI')
registerT12S.inputs.dof = int(12)
registerT12S.inputs.reference = template
registerT12S.inputs.in_file = epireg.inputs.t1_brain
#--- 5) Concatenate the two transformation matrices from 3 and 4.
concatxfm = pe.Node(interface=fslbase.ConvertXFM(), name='CONCATMATRICES')
concatxfm.inputs.concat_xfm = bool(1)
#--- 6) Register the EPI to the standard, using the combined transformation matrix
registerF2S = pe.Node(interface=fsl.ApplyXFM(), name='REGISTEREDF2MNI')
registerF2S.inputs.reference = template
registerF2S.inputs.in_file = epireg.inputs.epi
#--- 7) Use ANTS to normalise the structural to the MNI
antsregfast = pe.Node(Registration(
args='--float',
collapse_output_transforms=True,
fixed_image=template,
initial_moving_transform_com=True,
output_inverse_warped_image=True,
output_warped_image=True,
sigma_units=['vox'] * 3,
transforms=['Rigid', 'Affine', 'SyN'],
terminal_output='file',
winsorize_lower_quantile=0.005,
winsorize_upper_quantile=0.995,
convergence_threshold=[1e-08, 1e-08, -0.01],
convergence_window_size=[20, 20, 5],
metric=['Mattes', 'Mattes', ['Mattes', 'CC']],
metric_weight=[1.0, 1.0, [0.5, 0.5]],
number_of_iterations=[[10000, 11110, 11110], [10000, 11110, 11110],
[100, 30, 20]],
radius_or_number_of_bins=[32, 32, [32, 4]],
sampling_percentage=[0.3, 0.3, [None, None]],
sampling_strategy=['Regular', 'Regular', [None, None]],
shrink_factors=[[3, 2, 1], [3, 2, 1], [4, 2, 1]],
smoothing_sigmas=[[4.0, 2.0, 1.0], [4.0, 2.0, 1.0], [1.0, 0.5, 0.0]],
transform_parameters=[(0.1, ), (0.1, ), (0.2, 3.0, 0.0)],
use_estimate_learning_rate_once=[True] * 3,
use_histogram_matching=[False, False, True],
write_composite_transform=True),
name='NORMSTRUCT')
#--- 8) Apply the same warping to the EPI
apply2mean = pe.Node(ApplyTransforms(args='--float',
input_image_type=3,
interpolation='Linear',
invert_transform_flags=[False],
num_threads=1,
reference_image=template,
terminal_output='file'),
name='NORMFUNC')
#--- 9) Also need an outputnode, since otherwise some outputs may be binned.
outputnode = pe.Node(interface=util.IdentityInterface(fields=[
'warped', 'structmat', 'funcmat', 'epimat', 'funcreg', 'structreg'
]),
name='outputnode')
#--- 10) Custom plotting functions.
def bplot(in_file, MNI):
from nilearn import image
from nilearn import plotting
import matplotlib
niftifiledim = len(image.load_img(in_file).shape)
display = plotting.plot_anat(template)
display.add_edges(in_file)
matplotlib.pyplot.show()
return niftifiledim
def bplotN(in_file, MNI):
from nilearn import image
from nilearn import plotting
import matplotlib
niftifiledim = len(image.load_img(in_file).shape)
display = plotting.plot_anat(MNI)
display.add_edges(in_file)
matplotlib.pyplot.show()
return niftifiledim
showregL = pe.Node(Function(input_names=['in_file', 'MNI'],
output_names=['niftifiledim'],
function=bplot),
name='SHOWREG')
showregNL = pe.Node(Function(input_names=['in_file', 'MNI'],
output_names=['niftifiledim'],
function=bplotN),
name='SHOWREG')
#--- 11) Setup workflow
workflow = pe.Workflow(name='NORMPIPE')
workflow.base_dir = NIFTIDIR
#--- 12) Connect nodes, depending on whether we want to do normalisation too.
if alsonorm == bool(0):
workflow.connect(epireg, 'epi2str_mat', outputnode, 'epimat')
workflow.connect(epireg, 'epi2str_mat', concatxfm, 'in_file')
workflow.connect(registerT12S, 'out_matrix_file', concatxfm,
'in_file2')
workflow.connect(concatxfm, 'out_file', registerF2S, 'in_matrix_file')
workflow.connect(registerT12S, 'out_matrix_file', outputnode,
'structmat')
workflow.connect(registerF2S, 'out_matrix_file', outputnode, 'funcmat')
workflow.connect(registerF2S, 'out_file', outputnode, 'funcreg')
workflow.connect(registerT12S, 'out_file', outputnode, 'structreg')
workflow.connect(registerT12S, 'out_file', showregL, 'in_file')
workflow.connect(inputnode, 'standard', showregL, 'MNI')
workflow.write_graph(graph2use='exec')
workflow.run()
elif alsonorm == bool(1):
workflow.connect(epireg, 'epi2str_mat', outputnode, 'epimat')
workflow.connect(epireg, 'epi2str_mat', concatxfm, 'in_file')
workflow.connect(registerT12S, 'out_matrix_file', concatxfm,
'in_file2')
workflow.connect(concatxfm, 'out_file', registerF2S, 'in_matrix_file')
workflow.connect(registerT12S, 'out_matrix_file', outputnode,
'structmat')
workflow.connect(registerF2S, 'out_matrix_file', outputnode, 'funcmat')
workflow.connect(registerF2S, 'out_file', outputnode, 'funcreg')
workflow.connect(registerT12S, 'out_file', outputnode, 'structreg')
workflow.connect(registerF2S, 'out_file', apply2mean, 'input_image')
workflow.connect(registerT12S, 'out_file', antsregfast, 'moving_image')
workflow.connect(antsregfast, 'warped_image', outputnode, 'warped')
workflow.connect([(antsregfast, apply2mean, [('composite_transform',
'transforms')])])
workflow.connect(antsregfast, 'warped_image', showregNL, 'in_file')
workflow.connect(inputnode, 'standard', showregNL, 'MNI')
workflow.write_graph(graph2use='exec')
workflow.run()
print "Node completed. Returning to intital directory\n"
os.chdir(INITDIR)
from nipype.interfaces.fsl import Info
Info.standard_image()
template_path = Info.standard_image('MNI152_T1_1mm_brain.nii.gz')