def nrrd2nii_pmap(in_file, output_prefix):
from os.path import abspath as opap
from nipype.interfaces.base import CommandLine
from nipype.utils.filemanip import split_filename
_, name, _ = split_filename(in_file)
out_vol = experiment_dir + '/' + output_prefix + '/' + ('%s.nii.gz' % name)
cmd = CommandLine(('DWIConvert --inputVolume %s --outputVolume %s'
' --conversionMode NrrdToFSL') % (in_file, out_vol))
print "NRRD->NIFTI:" + cmd.cmd
cmd.run()
return opap(out_vol), opap(out_bval), opap(out_bvec)
def nrrd2nii_pmap(in_file, output_prefix):
from os.path import abspath as opap
from nipype.interfaces.base import CommandLine
from nipype.utils.filemanip import split_filename
_, name, _ = split_filename(in_file)
out_vol = experiment_dir + '/' + output_prefix + '/' + ('%s.nii.gz' % name)
cmd = CommandLine(('DWIConvert --inputVolume %s --outputVolume %s'
' --conversionMode NrrdToFSL') % (in_file, out_vol))
print "NRRD->NIFTI:" + cmd.cmd
cmd.run()
return opap(out_vol), opap(out_bval), opap(out_bvec)
def nrrd2nii(in_file):
from os.path import abspath as opap
from nipype.interfaces.base import CommandLine
from nipype.utils.filemanip import split_filename
_, name, _ = split_filename(in_file)
out_vol = '%s.nii.gz' % name
out_bval = '%s.bval' % name
out_bvec = '%s.bvec' % name
cmd = CommandLine(
('DWIConvert --inputVolume %s --outputVolume %s --outputBValues %s'
' --outputBVectors %s --conversionMode NrrdToFSL') %
(in_file, out_vol, out_bval, out_bvec))
cmd.run()
return opap(out_vol), opap(out_bval), opap(out_bvec)
def create_realign_reference(run, whichvol_glob, name="realignref"):
"""
run (int): run's number
whichvol_glob: 'first' or 'middle' or 'last' or
'mean', if 'mean' was chosed for run then whichvol_glob does't matter
"""
realignref = Workflow(name=name)
inputnode = Node(interface=util.IdentityInterface(fields=["in_sub", "in_hand"]), name="inputspec")
ds = Node(DataGrabber(infields=["subject_id", "hand"], outfields=["func"]), name="datasource")
ds.inputs.base_directory = opap(base_directory)
ds.inputs.template = "%s/%s_Hand/*.nii*"
ds.inputs.sort_filelist = True
# ds.inputs.subject_id = 'GK011RZJA'
# ds.inputs.hand = 'Left'
realignref.connect(inputnode, "in_hand", ds, "hand")
realignref.connect(inputnode, "in_sub", ds, "subject_id")
img2float = MapNode(
interface=fsl.ImageMaths(out_data_type="float", op_string="", suffix="_dtype"),
iterfield=["in_file"],
name="img2float",
)
realignref.connect(ds, ("func", pickrun), img2float, "in_file")
# realignref.connect(inputnode, 'in_files', img2float, 'in_file')
if whichvol_glob != "mean":
extract_ref = Node(interface=fsl.ExtractROI(t_size=1), iterfield=["in_file"], name="extractref")
realignref.connect(img2float, ("out_file", pickfirst), extract_ref, "in_file")
realignref.connect(img2float, ("out_file", pickvol, 0, whichvol_glob), extract_ref, "t_min")
outputnode = pe.Node(interface=util.IdentityInterface(fields=["ref_vol"]), name="outputnode")
if whichvol_glob != "mean":
realignref.connect(extract_ref, "roi_file", outputnode, "ref_vol")
else:
meanfunc = pe.Node(interface=fsl.ImageMaths(op_string="-Tmean", suffix="_mean"), name="meanfunc")
realignref.connect(img2float, ("out_file", pickfirst), meanfunc, "in_file")
realignref.connect(meanfunc, "out_file", outputnode, "ref_vol")
return realignref
###############################################################################
#
# DATA GRABBER NODE
#
###############################################################################
from nipype.interfaces.io import DataGrabber
from os.path import abspath as opap
base_directory = '/Users/AClab/Documents/mikbuch/Maestro_Project1'
ds = Node(DataGrabber(
infields=['subject_id', 'hand'], outfields=['func']), name='datasource'
)
ds.inputs.base_directory = opap(base_directory)
ds.inputs.template = '%s/%s_Hand/*.nii'
ds.inputs.sort_filelist = True
ds.inputs.subject_id = 'GK011RZJA'
ds.inputs.hand = 'Left'
'''
To print the list of files being taken uncomment the following lines.
'''
# functional_input = ds.run().outputs
# input_files = functional_input.get()['func']
# print input_files
###############################################################################
#
###############################################################################
#
# DATA GRABBER NODE
#
###############################################################################
from nipype.interfaces.io import DataGrabber
from os.path import abspath as opap
ds = Node(DataGrabber(
infields=['subject_id', 'hand'], outfields=['func']), name='datasource'
)
ds.inputs.base_directory = opap(base_directory)
ds.inputs.template = '%s/%s_Hand/*.nii*'
ds.inputs.sort_filelist = True
# ds.inputs.subject_id = 'GK011RZJA'
# ds.inputs.hand = 'Left'
featreg_merge.connect(inputnode, 'in_hand', ds, 'hand')
featreg_merge.connect(inputnode, 'in_sub', ds, 'subject_id')
'''
To print the list of files being taken uncomment the following lines.
'''
# functional_input = ds.run().outputs
# input_files = functional_input.get()['func']
# print input_files
############################################################################### # # MASK MULTIPLE WORKFLOW # ############################################################################### from nipype.pipeline import Workflow, Node import nipype.interfaces.io as nio from os.path import abspath as opap mask_multiple = Workflow(name='mask_multiple') grabber = nio.DataGrabber() grabber.inputs.base_directory = opap(base_directory) grabber.inputs.template = '*.nii*' grabber.inputs.sort_filelist = True grabbed = grabber.run() rois_filelist = grabbed.outputs.outfiles ############################################################################### # # MASK SINGLE WORKFLOW # ############################################################################### apply_mask_multiple = Workflow(name='apply_mask_multiple') import nipype.interfaces.utility as util inputnode = Node(
###############################################################################
#
# DATA GRABBER NODE
#
###############################################################################
from nipype.interfaces.io import DataGrabber
from os.path import abspath as opap
grabber = Node(DataGrabber(
infields=['subject_id', 'hand'],
outfields=['reference', 'matrix']),
name='moloch'
)
grabber.inputs.base_directory = opap(base_directory)
grabber.inputs.template = '*'
reg_dir_template = '%s/Analyzed_Data/Main*Exp_%sHand_Run-3.feat/reg/'
grabber.inputs.field_template = dict(
reference=reg_dir_template + 'example_func.nii.gz',
matrix=reg_dir_template + 'standard2example*'
)
grabber.inputs.template_args = dict(
reference=[['subject_id', 'hand']],
matrix=[['subject_id', 'hand']]
)
grabber.inputs.sort_filelist = True
flirt_apply_all_subs.connect(
inputsub, 'sub',
def create_mvpa_preproc(
base_directory,
datasink_directory,
workflow_base_directory,
subject_template,
name="mvpapreproc",
run=1,
whichvol_glob="mean",
):
mvpapreproc = pe.Workflow(name=name)
inputsub = Node(interface=util.IdentityInterface(fields=["sub"]), name="inputsub")
# inputsub.inputs.sub = ['GK011RZJA', 'GK012OHPA']
# inputsub.iterables = ('sub', ['GK011RZJA', 'GK012OHPA'])
inputsub.iterables = ("sub", get_subject_names(base_directory, subject_template))
inputhand = Node(interface=util.IdentityInterface(fields=["hand"]), name="inputhand")
inputhand.iterables = ("hand", ["Left", "Right"])
# ### REFERENCE EXTRACTION ################################################
reference = create_realign_reference(run=run, whichvol_glob=whichvol_glob)
mvpapreproc.connect(inputsub, "sub", reference, "inputspec.in_sub")
mvpapreproc.connect(inputhand, "hand", reference, "inputspec.in_hand")
# featreg_merge workflow
merge = create_featreg_merge(run=run, whichvol_glob=whichvol_glob)
mvpapreproc.connect(inputsub, "sub", merge, "inputspec.in_sub")
mvpapreproc.connect(inputhand, "hand", merge, "inputspec.in_hand")
mvpapreproc.connect(reference, "outputnode.ref_vol", merge, "featpreproc.realign.ref_file")
###########################################################################
#
# DATA SINK NODE
#
###########################################################################
from nipype.interfaces.utility import Function
add_two_strings_node = Node(
interface=Function(input_names=["subject", "hand"], output_names=["sub_hand_name"], function=add_two_strings),
name="ats",
)
"""
If iterating trought hands will be available
"""
mvpapreproc.connect(inputsub, "sub", add_two_strings_node, "subject")
mvpapreproc.connect(inputhand, "hand", add_two_strings_node, "hand")
from nipype.interfaces.io import DataSink
datasink = Node(interface=DataSink(), name="datasink")
datasink.inputs.base_directory = opap(datasink_directory)
datasink.inputs.parameterization = False
mvpapreproc.connect(add_two_strings_node, "sub_hand_name", datasink, "container")
mvpapreproc.connect(
merge,
"merge.merged_file",
# datasink, ds.inputs.subject_id + '/' + ds.inputs.hand + '_Hand/mvpa'
datasink,
"preprocessed",
)
# mvpa_preproc.connect(inputsub, 'sub', datasink, 'container')
datasink_masks = Node(interface=DataSink(), name="datasink_masks")
datasink_masks.inputs.base_directory = opap(datasink_directory)
datasink_masks.inputs.parameterization = False
datasink_masks.inputs.substitutions = [("", ""), ("vol0000", "mask")]
mvpapreproc.connect(add_two_strings_node, "sub_hand_name", datasink_masks, "container")
mvpapreproc.connect(merge, ("splitnode.out_files", pickfirst), datasink_masks, "preprocessed")
###########################################################################
#
# BASE_DIR, GRAPH, AND RUN
#
###########################################################################
mvpapreproc.base_dir = workflow_base_directory
# mvpa_preproc.base_dir = \
# '/Users/AClab/Documents/mikbuch/Maestro_Project1/mvpa/preprocessing/'
return mvpapreproc
def create_featreg_merge(run, whichvol_glob, name="featregmerge"):
###########################################################################
#
# FEATREG_MERGE WORKFLOW
#
###########################################################################
featregmerge = Workflow(name=name)
inputnode = Node(
interface=util.IdentityInterface(fields=["in_sub", "in_hand", "run", "whichvol_glob"]), name="inputspec"
)
# inputnode.inputs.in_sub = 'GK011RZJA'
###########################################################################
#
# DATA GRABBER NODE
#
###########################################################################
ds = Node(DataGrabber(infields=["subject_id", "hand"], outfields=["func"]), name="datasource")
ds.inputs.base_directory = opap(base_directory)
ds.inputs.template = "%s/%s_Hand/*.nii*"
ds.inputs.sort_filelist = True
# ds.inputs.subject_id = 'GK011RZJA'
# ds.inputs.hand = 'Left'
featregmerge.connect(inputnode, "in_hand", ds, "hand")
featregmerge.connect(inputnode, "in_sub", ds, "subject_id")
"""
To print the list of files being taken uncomment the following lines.
"""
# functional_input = ds.run().outputs
# input_files = functional_input.get()['func']
# print input_files
###########################################################################
#
# CREATE FEAT REGISTRATION WORKFLOW NODE
#
###########################################################################
preproc = create_featreg_preproc(highpass=True, whichvol="first")
preproc.inputs.inputspec.fwhm = 0
preproc.inputs.inputspec.highpass = 128.0 / (2 * 2.5)
# remove_nodes takes list as an argument
preproc.remove_nodes([preproc.get_node("extractref")])
"""
preproc.disconnect(
preproc.get_node('extractref'), 'roi_file',
preproc.get_node('realign'), 'ref_file'
)
"""
featregmerge.connect(ds, "func", preproc, "inputspec.func")
###########################################################################
#
# MERGE NODE
#
###########################################################################
merge = Node(
interface=fsl.utils.Merge(dimension="t", output_type="NIFTI_GZ", merged_file="bold.nii.gz"), name="merge"
)
featregmerge.connect(preproc, "outputspec.highpassed_files", merge, "in_files")
masksnode = Node(
interface=fsl.utils.Merge(dimension="t", output_type="NIFTI_GZ", merged_file="masks_merged.nii.gz"),
name="masksnode",
)
featregmerge.connect(preproc, "outputspec.mask", masksnode, "in_files")
# ### SPLIT MERGED MASKS ##################################################
splitnode = Node(interface=fsl.utils.Split(dimension="t", output_type="NIFTI_GZ"), name="splitnode")
featregmerge.connect(masksnode, "merged_file", splitnode, "in_file")
return featregmerge
from nipype.interfaces.io import DataGrabber
from nipype.pipeline import Node
from os.path import abspath as opap
ds = Node(DataGrabber(
infields=['subject_id'], outfields=['func']), name='datasource'
)
ds.inputs.base_directory = opap('ds105')
ds.inputs.template = '%s/BOLD/task001*/bold.nii.gz'
ds.inputs.sort_filelist = True
ds.inputs.subject_id = 'sub001'
functional_input = ds.run().outputs
input_files = functional_input.get()['func']
print input_files
preproc.inputs.inputspec.highpass = 128. / (2 * 2.5)
###############################################################################
#
# DATA GRABBER NODE
#
###############################################################################
from nipype.interfaces.io import DataGrabber
from os.path import abspath as opap
base_directory = '/Users/AClab/Documents/mikbuch/Maestro_Project1'
ds = Node(DataGrabber(infields=['subject_id', 'hand'], outfields=['func']),
name='datasource')
ds.inputs.base_directory = opap(base_directory)
ds.inputs.template = '%s/%s_Hand/*.nii'
ds.inputs.sort_filelist = True
ds.inputs.subject_id = 'GK011RZJA'
ds.inputs.hand = 'Left'
'''
To print the list of files being taken uncomment the following lines.
'''
# functional_input = ds.run().outputs
# input_files = functional_input.get()['func']
# print input_files
###############################################################################
#
# MERGE NODE
#
