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Merged
merged 3 commits into from
Sep 12, 2013
Merged

Fix/atlasupdate #653

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ac38645
enh: updated mindboggle atlases
satra Sep 12, 2013
d6b27a2
fix: missing template
satra Sep 12, 2013
377cacd
enh: allow naming a workflow
satra Sep 12, 2013
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21 changes: 11 additions & 10 deletions examples/rsfmri_preprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,15 +33,15 @@

specifically the 2mm versions of:

- `Joint Fusion Atlas <http://mindboggle.info/data/atlases/jointfusion/OASIS-TRT-20_DKT31_CMA_jointfusion_labels_in_MNI152_2mm.nii.gz>`_
- `MNI template <http://mindboggle.info/data/templates/ants/OASIS-TRT-20_template_in_MNI152_2mm.nii.gz>`_
- `Joint Fusion Atlas <http://mindboggle.info/data/atlases/jointfusion/OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_2mm.nii.gz>`_
- `MNI template <http://mindboggle.info/data/templates/ants/OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz>`_

The 2mm version was generated with::

>>> from nipype import freesurfer as fs
>>> rs = fs.Resample()
>>> rs.inputs.in_file = 'OASIS-TRT-20_DKT31_CMA_jointfusion_labels_in_MNI152.nii.gz'
>>> rs.inputs.resampled_file = 'OASIS-TRT-20_DKT31_CMA_jointfusion_labels_in_MNI152_2mm.nii.gz'
>>> rs.inputs.in_file = 'OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152.nii.gz'
>>> rs.inputs.resampled_file = 'OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_2mm.nii.gz'
>>> rs.inputs.voxel_size = (2., 2., 2.)
>>> rs.inputs.args = '-rt nearest -ns 1'
>>> res = rs.run()
Expand Down Expand Up @@ -584,7 +584,7 @@ def create_workflow(files,
reg.inputs.use_histogram_matching = [False] * 3 + [True]
reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
reg.inputs.fixed_image = \
os.path.abspath('OASIS-TRT-20_template_to_MNI152_2mm.nii.gz')
os.path.abspath('OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz')
reg.inputs.num_threads = 4
reg.plugin_args = {'qsub_args': '-l nodes=1:ppn=4'}

Expand Down Expand Up @@ -625,7 +625,7 @@ def create_workflow(files,
sample2mni.inputs.interpolation = 'BSpline'
sample2mni.inputs.invert_transform_flags = [False, False]
sample2mni.inputs.reference_image = \
os.path.abspath('OASIS-TRT-20_template_to_MNI152_2mm.nii.gz')
os.path.abspath('OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz')
sample2mni.inputs.terminal_output = 'file'
wf.connect(bandpass, 'out_file', sample2mni, 'input_image')
wf.connect(merge, 'out', sample2mni, 'transforms')
Expand All @@ -641,8 +641,8 @@ def create_workflow(files,
ts2txt.inputs.indices = [8] + range(10, 14) + [17, 18, 26, 47] +\
range(49, 55) + [58]
ts2txt.inputs.label_file = \
os.path.abspath(('OASIS-TRT-20_DKT31_CMA_jointfusion_labels_in_MNI152'
'_2mm.nii.gz'))
os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
'2mm.nii.gz'))
wf.connect(sample2mni, 'output_image', ts2txt, 'timeseries_file')

# Save the relevant data into an output directory
Expand Down Expand Up @@ -699,7 +699,7 @@ def create_workflow(files,
"""


def create_resting_workflow(args):
def create_resting_workflow(args, name='resting'):
TR = args.TR
slice_times = args.slice_times
slice_thickness = None
Expand All @@ -722,7 +722,8 @@ def create_resting_workflow(args):
slice_thickness=slice_thickness,
lowpass_freq=args.lowpass_freq,
highpass_freq=args.highpass_freq,
sink_directory=os.path.abspath(args.sink))
sink_directory=os.path.abspath(args.sink),
name=name)
if args.field_maps:
kwargs.update(**dict(fieldmap_images=args.field_maps,
FM_TEdiff=args.TE_diff,
Expand Down