diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py index 92fad77100..eeab08371e 100644 --- a/nipype/interfaces/fsl/epi.py +++ b/nipype/interfaces/fsl/epi.py @@ -608,16 +608,13 @@ class EddyInputSpec(FSLCommandInputSpec): field = File( exists=True, argstr="--field=%s", - desc=("Non-topup derived fieldmap scaled in Hz"), + desc="Non-topup derived fieldmap scaled in Hz", ) field_mat = File( exists=True, argstr="--field_mat=%s", - desc=( - "Matrix specifying the relative positions of " - "the fieldmap, --field, and the first volume " - "of the input file, --imain" - ), + desc="Matrix specifying the relative positions of the fieldmap, " + "--field, and the first volume of the input file, --imain", ) flm = traits.Enum( @@ -656,26 +653,26 @@ class EddyInputSpec(FSLCommandInputSpec): default_value=1000, usedefault=True, argstr="--nvoxhp=%s", - desc=("# of voxels used to estimate the " "hyperparameters"), + desc="# of voxels used to estimate the hyperparameters", ) fudge_factor = traits.Float( default_value=10.0, usedefault=True, argstr="--ff=%s", - desc=("Fudge factor for hyperparameter " "error variance"), + desc="Fudge factor for hyperparameter error variance", ) dont_sep_offs_move = traits.Bool( False, argstr="--dont_sep_offs_move", - desc=("Do NOT attempt to separate " "field offset from subject " "movement"), + desc="Do NOT attempt to separate field offset from subject movement", ) dont_peas = traits.Bool( False, argstr="--dont_peas", - desc="Do NOT perform a post-eddy alignment of " "shells", + desc="Do NOT perform a post-eddy alignment of shells", ) fwhm = traits.Float( - desc=("FWHM for conditioning filter when estimating " "the parameters"), + desc="FWHM for conditioning filter when estimating the parameters", argstr="--fwhm=%s", ) niter = traits.Int( @@ -686,7 +683,7 @@ class EddyInputSpec(FSLCommandInputSpec): "lsr", usedefault=True, argstr="--resamp=%s", - desc=("Final resampling method (jacobian/least " "squares)"), + desc="Final resampling method (jacobian/least squares)", ) repol = traits.Bool( @@ -735,9 +732,7 @@ class EddyInputSpec(FSLCommandInputSpec): 1, -1, argstr="--mb_offs=%d", - desc=( - "Multi-band offset (-1 if bottom slice removed, 1 if " "top slice removed" - ), + desc="Multi-band offset (-1 if bottom slice removed, 1 if top slice removed", requires=["multiband_factor"], min_ver="5.0.10", ) @@ -816,11 +811,8 @@ class EddyInputSpec(FSLCommandInputSpec): is_shelled = traits.Bool( False, argstr="--data_is_shelled", - desc=( - "Override internal check to ensure that " - "date are acquired on a set of b-value " - "shells" - ), + desc="Override internal check to ensure that date are acquired " + "on a set of b-value shells", ) use_cuda = traits.Bool(False, desc="Run eddy using cuda gpu") @@ -838,9 +830,7 @@ class EddyOutputSpec(TraitedSpec): ) out_parameter = File( exists=True, - desc=( - "Text file with parameters defining the field and" "movement for each scan" - ), + desc="Text file with parameters defining the field and movement for each scan", ) out_rotated_bvecs = File( exists=True, desc="File containing rotated b-values for all volumes" @@ -855,74 +845,56 @@ class EddyOutputSpec(TraitedSpec): ) out_shell_alignment_parameters = File( exists=True, - desc=( - "Text file containing rigid body movement parameters " - "between the different shells as estimated by a " - "post-hoc mutual information based registration" - ), + desc="Text file containing rigid body movement parameters " + "between the different shells as estimated by a " + "post-hoc mutual information based registration", ) out_shell_pe_translation_parameters = File( exists=True, - desc=( - "Text file containing translation along the PE-direction " - "between the different shells as estimated by a " - "post-hoc mutual information based registration" - ), + desc="Text file containing translation along the PE-direction " + "between the different shells as estimated by a " + "post-hoc mutual information based registration", ) out_shell_pe_translation_parameters = File( exists=True, - desc=( - "Text file containing translation along the PE-direction " - "between the different shells as estimated by a " - "post-hoc mutual information based registration" - ), + desc="Text file containing translation along the PE-direction " + "between the different shells as estimated by a " + "post-hoc mutual information based registration", ) out_outlier_map = File( exists=True, - desc=( - "Matrix where rows represent volumes and columns represent " - 'slices. "0" indicates that scan-slice is not an outlier ' - 'and "1" indicates that it is' - ), + desc="Matrix where rows represent volumes and columns represent " + 'slices. "0" indicates that scan-slice is not an outlier ' + 'and "1" indicates that it is', ) out_outlier_n_stdev_map = File( exists=True, - desc=( - "Matrix where rows represent volumes and columns represent " - "slices. Values indicate number of standard deviations off the " - "mean difference between observation and prediction is" - ), + desc="Matrix where rows represent volumes and columns represent " + "slices. Values indicate number of standard deviations off the " + "mean difference between observation and prediction is", ) out_outlier_n_sqr_stdev_map = File( exists=True, - desc=( - "Matrix where rows represent volumes and columns represent " - "slices. Values indicate number of standard deivations off the " - "square root of the mean squared difference between observation " - "and prediction is" - ), + desc="Matrix where rows represent volumes and columns represent " + "slices. Values indicate number of standard deivations off the " + "square root of the mean squared difference between observation " + "and prediction is", ) out_outlier_report = File( exists=True, - desc=( - "Text file with a plain language report on what " - "outlier slices eddy has found" - ), + desc="Text file with a plain language report on what " + "outlier slices eddy has found", ) out_outlier_free = File( exists=True, - desc=( - "4D image file not corrected for susceptibility or eddy-" - "current distortions or subject movement but with outlier " - "slices replaced" - ), + desc="4D image file not corrected for susceptibility or eddy-" + "current distortions or subject movement but with outlier " + "slices replaced", ) out_movement_over_time = File( exists=True, - desc=( - "Text file containing translations (mm) and rotations " - "(radians) for each excitation" - ), + desc="Text file containing translations (mm) and rotations " + "(radians) for each excitation", ) out_cnr_maps = File(exists=True, desc="path/name of file with the cnr_maps") out_residuals = File(exists=True, desc="path/name of file with the residuals")