def smooth_data(name='func_smoothed'):
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.utility as util
import nipype.interfaces.fsl as fsl
flow = Workflow(name)
inputnode = Node(util.IdentityInterface(fields=['func_data']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['func_smoothed']),
name='outputnode')
smooth = Node(interface=fsl.Smooth(), name='func_smooth_fwhm_4')
smooth.inputs.fwhm = 4.0
smooth.terminal_output = 'file'
flow.connect(inputnode, 'func_data', smooth, 'in_file')
flow.connect(smooth, 'smoothed_file', outputnode, 'func_smoothed')
return flow
def smooth_data(name = 'func_smoothed'):
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.utility as util
import nipype.interfaces.fsl as fsl
flow = Workflow(name)
inputnode = Node(util.IdentityInterface(fields=['func_data']),
name = 'inputnode')
outputnode = Node(util.IdentityInterface(fields=['func_smoothed']),
name = 'outputnode')
smooth = Node(interface=fsl.Smooth(), name='func_smooth_fwhm_4')
smooth.inputs.fwhm = 4.0
smooth.terminal_output = 'file'
flow.connect(inputnode, 'func_data' , smooth , 'in_file' )
flow.connect(smooth, 'smoothed_file' , outputnode , 'func_smoothed' )
return flow
if do_recon_all:
# two version of recon-all : fs5 and fs6 commands
if fsversion == "freesurfer5":
if not checkfsVersion("v5"):
raise Exception("If I may .. you are using freesurfer 6.0 and requested a freesurfer5 command of recon-all")
# we actually do the recon-all
fsReconAll = Node(AbcReconAll(), name="fsReconAll5")
fsReconAll.inputs.args = ' -3T -contrasurfreg -qcache -no-isrunning'
fsReconAll.inputs.directive = 'all'
fsReconAll.inputs.environ = {}
fsReconAll.ignore_exception = False
fsReconAll.inputs.subjects_dir = subjects_dir
fsReconAll.terminal_output = 'stream'
fsReconAll.inputs.use_FLAIR = use_FLAIR
# no need to connect the T1 and T2flair since the process was already initialized in basic_structural
ishanat.connect(struct, "outputNode.subject_id", fsReconAll, "subject_id")
else:
if not checkfsVersion("v6"):
raise Exception("If I may .. you are using some freesurfer 5 version and requested a freesurfer6 command of recon-all")
# Node: fs.fsReconAll
fsReconAll = Node(AbcReconAll(), name="fsReconAll6")
fsReconAll.inputs.args = ' -brainstem-structures -3T -contrasurfreg -qcache -no-isrunning'
fsReconAll.inputs.directive = 'all'
fsReconAll.inputs.environ = {}
fsReconAll.ignore_exception = True # may throw an exception that cannot find result files ==> dummy
