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NF: allow to select last volume for MC, various DOC tune ups #1141

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merged 1 commit into from
Sep 9, 2015
Merged

NF: allow to select last volume for MC, various DOC tune ups #1141

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15 changes: 9 additions & 6 deletions nipype/workflows/fmri/fsl/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,10 @@ def pickvol(filenames, fileidx, which):
idx = 0
elif which.lower() == 'middle':
idx = int(np.ceil(load(filenames[fileidx]).get_shape()[3]/2))
elif which.lower() == 'last':
idx = load(filenames[fileidx]).get_shape()[3]-1
else:
raise Exception('unknown value for volume selection : %s'%which)
raise Exception('unknown value for volume selection : %s' % which)
return idx

def getbtthresh(medianvals):
Expand Down Expand Up @@ -381,7 +383,7 @@ def create_featreg_preproc(name='featpreproc', highpass=True, whichvol='middle')

name : name of workflow (default: featpreproc)
highpass : boolean (default: True)
whichvol : which volume of the first run to register to ('first', 'middle', 'mean')
whichvol : which volume of the first run to register to ('first', 'middle', 'last', 'mean')

Inputs::

Expand Down Expand Up @@ -467,6 +469,7 @@ def create_featreg_preproc(name='featpreproc', highpass=True, whichvol='middle')
run.
"""


img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string = '',
suffix='_dtype'),
Expand All @@ -475,7 +478,7 @@ def create_featreg_preproc(name='featpreproc', highpass=True, whichvol='middle')
featpreproc.connect(inputnode, 'func', img2float, 'in_file')

"""
Extract the first volume of the first run as the reference
Extract the middle (or what whichvol points to) volume of the first run as the reference
"""

if whichvol != 'mean':
Expand All @@ -488,7 +491,7 @@ def create_featreg_preproc(name='featpreproc', highpass=True, whichvol='middle')


"""
Realign the functional runs to the reference (1st volume of first run)
Realign the functional runs to the reference (`whichvol` volume of first run)
"""

motion_correct = pe.MapNode(interface=fsl.MCFLIRT(save_mats = True,
Expand Down Expand Up @@ -518,7 +521,7 @@ def create_featreg_preproc(name='featpreproc', highpass=True, whichvol='middle')
featpreproc.connect(plot_motion, 'out_file', outputnode, 'motion_plots')

"""
Extract the mean volume of the first functional run
Extract the mean volume of the first functional runpreproc
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extra preproc

"""

meanfunc = pe.Node(interface=fsl.ImageMaths(op_string = '-Tmean',
Expand Down Expand Up @@ -1093,7 +1096,7 @@ def create_fsl_fs_preproc(name='preproc', highpass=True, whichvol='middle'):
return featpreproc

def create_reg_workflow(name='registration'):
"""Create a FEAT preprocessing workflow together with freesurfer
"""Create a FEAT preprocessing workflow

Parameters
----------
Expand Down