@@ -53,7 +53,9 @@ class GTMSegInputSpec(FSTraitedSpec):
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usedefault = True ,
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)
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- upsampling_factor = traits .Int (argstr = "--usf %i" , desc = "upsampling factor (default is 2)" )
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+ upsampling_factor = traits .Int (
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+ argstr = "--usf %i" , desc = "upsampling factor (default is 2)"
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+ )
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subsegwm = traits .Bool (
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argstr = "--subsegwm" , desc = "subsegment WM into lobes (default)"
@@ -139,7 +141,10 @@ class GTMSeg(FSCommand):
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def _list_outputs (self ):
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outputs = self .output_spec ().get ()
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outputs ['gtm_file' ] = os .path .join (
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- self .inputs .subjects_dir , self .inputs .subject_id , 'mri' , self .inputs .out_file
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+ self .inputs .subjects_dir ,
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+ self .inputs .subject_id ,
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+ 'mri' ,
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+ self .inputs .out_file ,
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)
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return outputs
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@@ -167,7 +172,7 @@ class GTMPVCInputSpec(FSTraitedSpec):
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desc = "segfile : anatomical segmentation to define regions for GTM" ,
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)
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- _reg_xor = ["reg_file" , "regheader" , "reg_identity" ]
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+ _reg_xor = ["reg_file" , "regheader" , "reg_identity" ]
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reg_file = File (
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exists = True ,
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argstr = "--reg %s" ,
@@ -372,7 +377,11 @@ class GTMPVCInputSpec(FSTraitedSpec):
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)
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opt_tol = traits .Tuple (
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- traits .Int , traits .Float , traits .Float , argstr = "--opt-tol %i %f %f" , desc = "n_iters_max ftol lin_min_tol : optimization parameters for adaptive gtm using fminsearch"
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+ traits .Int ,
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+ traits .Float ,
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+ traits .Float ,
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+ argstr = "--opt-tol %i %f %f" ,
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+ desc = "n_iters_max ftol lin_min_tol : optimization parameters for adaptive gtm using fminsearch" ,
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)
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opt_brain = traits .Bool (argstr = "--opt-brain" , desc = "apply adaptive GTM" )
@@ -420,15 +429,11 @@ class GTMPVCOutputSpec(TraitedSpec):
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mgx_gm = File (
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desc = "All GM voxel-wise values corrected using the extended Muller-Gartner method" ,
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)
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- rbv = File (
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- desc = "All GM voxel-wise values corrected using the RBV method"
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- )
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+ rbv = File (desc = "All GM voxel-wise values corrected using the RBV method" )
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opt_params = File (
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desc = "Optimal parameter estimates for the FWHM using adaptive GTM"
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)
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- yhat0 = File (
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- desc = "4D PET file of signal estimate (yhat) after PVC (unsmoothed)"
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- )
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+ yhat0 = File (desc = "4D PET file of signal estimate (yhat) after PVC (unsmoothed)" )
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yhat = File (
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desc = "4D PET file of signal estimate (yhat) after PVC (smoothed with PSF)" ,
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)
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