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Correct Class Segment in spm.preprocess #580

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Merged
merged 3 commits into from
Jun 15, 2013
Merged

Correct Class Segment in spm.preprocess #580

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4961f3d
Segment in SPM interface throws error.
mick-d Jun 11, 2013
dfb33ba
In Segment, include bias-corrected output only if corresponding save_…
mick-d Jun 12, 2013
db46c6a
Add deprecation for old output variable modulated_input_image in Segm…
mick-d Jun 12, 2013
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24 changes: 13 additions & 11 deletions nipype/interfaces/spm/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -518,16 +518,17 @@ class SegmentInputSpec(SPMCommandInputSpec):


class SegmentOutputSpec(TraitedSpec):
native_gm_image = File(exists=True, desc='native space grey probability map')
normalized_gm_image = File(exists=True, desc='normalized grey probability map',)
modulated_gm_image = File(exists=True, desc='modulated, normalized grey probability map')
native_wm_image = File(exists=True, desc='native space white probability map')
normalized_wm_image = File(exists=True, desc='normalized white probability map')
modulated_wm_image = File(exists=True, desc='modulated, normalized white probability map')
native_csf_image = File(exists=True, desc='native space csf probability map')
normalized_csf_image = File(exists=True, desc='normalized csf probability map')
modulated_csf_image = File(exists=True, desc='modulated, normalized csf probability map')
modulated_input_image = File(exists=True, desc='modulated version of input image')
native_gm_image = File(desc='native space grey probability map')
normalized_gm_image = File(desc='normalized grey probability map',)
modulated_gm_image = File(desc='modulated, normalized grey probability map')
native_wm_image = File(desc='native space white probability map')
normalized_wm_image = File(desc='normalized white probability map')
modulated_wm_image = File(desc='modulated, normalized white probability map')
native_csf_image = File(desc='native space csf probability map')
normalized_csf_image = File(desc='normalized csf probability map')
modulated_csf_image = File(desc='modulated, normalized csf probability map')
modulated_input_image = File(deprecated='0.10', new_name='bias_corrected_image', desc='bias-corrected version of input image')
bias_corrected_image = File(desc='bias-corrected version of input image')
transformation_mat = File(exists=True, desc='Normalization transformation')
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Only transformation_mat and inverse_transformation_mat are not predicated by inputs, so File(exists=True) remains for these outputs

inverse_transformation_mat = File(exists=True, desc='Inverse normalization info')

Expand Down Expand Up @@ -583,7 +584,8 @@ def _list_outputs(self):
if getattr(self.inputs, outtype)[idx]:
outfield = '%s_%s_image'%(image,tissue)
outputs[outfield] = fname_presuffix(f, prefix='%sc%d'%(prefix,tidx+1))
outputs['modulated_input_image'] = fname_presuffix(f, prefix='m')
if isdefined(self.inputs.save_bias_corrected) and self.inputs.save_bias_corrected:
outputs['bias_corrected_image'] = fname_presuffix(f, prefix='m')
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The new variable bias_corrected_image is used in this line of code

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i'll have to run this to test, but with the deprecated flag do you know if outputs['modulated_input_image'] is set or not when the interface returns?

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When i used outputs['modulated_input_image'] instead of outputs['bias_corrected_image'] (both with the deprecated flag update already in place) then it didn't work (can't remember what was wrong). But with the code as shown above then no matter the boolean value of save_bias_corrected, the interface run fine.

Does that answer your question? Or would you need me to run the interface as shown above and see the value of outputs['modulated_input_image']?

t_mat = fname_presuffix(f, suffix='_seg_sn.mat', use_ext=False)
outputs['transformation_mat'] = t_mat
invt_mat = fname_presuffix(f, suffix='_seg_inv_sn.mat', use_ext=False)
Expand Down