@@ -119,7 +119,7 @@ class AlignEpiAnatPyOutputSpec(TraitedSpec):
119119 desc = "matrix to volume register and align epi"
120120 "to anatomy and put into standard space" )
121121 epi_vr_motion = File (
122- desc = "motion parameters from EPI time-series"
122+ desc = "motion parameters from EPI time-series"
123123 "registration (tsh included in name if slice"
124124 "timing correction is also included)." )
125125 skullstrip = File (
@@ -131,20 +131,20 @@ class AlignEpiAnatPy(AFNIPythonCommand):
131131 an EPI and an anatomical structural dataset, and applies the resulting
132132 transformation to one or the other to bring them into alignment.
133133
134- This script computes the transforms needed to align EPI and
135- anatomical datasets using a cost function designed for this purpose. The
136- script combines multiple transformations, thereby minimizing the amount of
134+ This script computes the transforms needed to align EPI and
135+ anatomical datasets using a cost function designed for this purpose. The
136+ script combines multiple transformations, thereby minimizing the amount of
137137 interpolation applied to the data.
138-
138+
139139 Basic Usage:
140140 align_epi_anat.py -anat anat+orig -epi epi+orig -epi_base 5
141-
141+
142142 The user must provide EPI and anatomical datasets and specify the EPI
143- sub-brick to use as a base in the alignment.
143+ sub-brick to use as a base in the alignment.
144144
145145 Internally, the script always aligns the anatomical to the EPI dataset,
146- and the resulting transformation is saved to a 1D file.
147- As a user option, the inverse of this transformation may be applied to the
146+ and the resulting transformation is saved to a 1D file.
147+ As a user option, the inverse of this transformation may be applied to the
148148 EPI dataset in order to align it to the anatomical data instead.
149149
150150 This program generates several kinds of output in the form of datasets
@@ -182,7 +182,7 @@ def _list_outputs(self):
182182 epi_prefix = '' .join (self ._gen_fname (self .inputs .in_file ).split ('+' )[:- 1 ])
183183 outputtype = self .inputs .outputtype
184184 if outputtype == 'AFNI' :
185- ext = '.HEAD'
185+ ext = '.HEAD'
186186 else :
187187 Info .output_type_to_ext (outputtype )
188188 matext = '.1D'
@@ -620,7 +620,7 @@ class AutoTLRCInputSpec(CommandLineInputSpec):
620620 mandatory = True ,
621621 exists = True ,
622622 copyfile = False )
623- base = traits .Str (
623+ base = traits .Str (
624624 desc = ' Reference anatomical volume'
625625 ' Usually this volume is in some standard space like'
626626 ' TLRC or MNI space and with afni dataset view of'
@@ -706,7 +706,7 @@ def _list_outputs(self):
706706 ext = '.HEAD'
707707 outputs ['out_file' ] = os .path .abspath (self ._gen_fname (self .inputs .in_file , suffix = '+tlrc' )+ ext )
708708 return outputs
709-
709+
710710class BandpassInputSpec (AFNICommandInputSpec ):
711711 in_file = File (
712712 desc = 'input file to 3dBandpass' ,
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