def test_SliceTimer_outputs(): output_map = dict(slice_time_corrected_file=dict(), ) outputs = SliceTimer.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_SliceTimer_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), index_dir=dict(argstr='--down', ), args=dict(argstr='%s', ), out_file=dict(argstr='--out=%s', hash_files=False, genfile=True, ), custom_timings=dict(argstr='--tcustom=%s', ), time_repetition=dict(argstr='--repeat=%f', ), slice_direction=dict(argstr='--direction=%d', ), custom_order=dict(argstr='--ocustom=%s', ), terminal_output=dict(mandatory=True, nohash=True, ), environ=dict(nohash=True, usedefault=True, ), in_file=dict(position=0, mandatory=True, argstr='--in=%s', ), global_shift=dict(argstr='--tglobal', ), output_type=dict(), interleaved=dict(argstr='--odd', ), ) inputs = SliceTimer.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value
def test_SliceTimer_inputs(): input_map = dict( args=dict(argstr='%s', ), custom_order=dict(argstr='--ocustom=%s', ), custom_timings=dict(argstr='--tcustom=%s', ), environ=dict( nohash=True, usedefault=True, ), global_shift=dict(argstr='--tglobal', ), ignore_exception=dict( nohash=True, usedefault=True, ), in_file=dict( argstr='--in=%s', mandatory=True, position=0, ), index_dir=dict(argstr='--down', ), interleaved=dict(argstr='--odd', ), out_file=dict( argstr='--out=%s', genfile=True, hash_files=False, ), output_type=dict(), slice_direction=dict(argstr='--direction=%d', ), terminal_output=dict( mandatory=True, nohash=True, ), time_repetition=dict(argstr='--repeat=%f', ), ) inputs = SliceTimer.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value
# Reorient to standard space using FSL reorientfunc = Node(Reorient2Std(), name='reorientfunc') reorientstruct = Node(Reorient2Std(), name='reorientstruct') # Reslice- using MRI_convert reslice = Node(MRIConvert(vox_size=resampled_voxel_size, out_type='nii'), name='reslice') # Segment structural scan #segment = Node(Segment(affine_regularization='none'), name='segment') segment = Node(FAST(no_bias=True, segments=True, number_classes=3), name='segment') #Slice timing correction based on interleaved acquisition using FSL slicetime_correct = Node(SliceTimer(interleaved=interleave, slice_direction=slice_dir, time_repetition=TR), name='slicetime_correct') # Motion correction motion_correct = Node(MCFLIRT(save_plots=True, mean_vol=True), name='motion_correct') # Registration- using FLIRT # The BOLD image is 'in_file', the anat is 'reference', the output is 'out_file' coreg1 = Node(FLIRT(), name='coreg1') coreg2 = Node(FLIRT(apply_xfm=True), name='coreg2') # make binary mask # structural is the 'in_file', output is 'binary_file' binarize_struct = Node(Binarize(dilate=mask_dilation,