@@ -119,7 +119,7 @@ class AlignEpiAnatPyOutputSpec(TraitedSpec):
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desc = "matrix to volume register and align epi"
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"to anatomy and put into standard space" )
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epi_vr_motion = File (
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- desc = "motion parameters from EPI time-series"
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+ desc = "motion parameters from EPI time-series"
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"registration (tsh included in name if slice"
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"timing correction is also included)." )
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skullstrip = File (
@@ -131,20 +131,20 @@ class AlignEpiAnatPy(AFNIPythonCommand):
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an EPI and an anatomical structural dataset, and applies the resulting
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transformation to one or the other to bring them into alignment.
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- This script computes the transforms needed to align EPI and
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- anatomical datasets using a cost function designed for this purpose. The
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- script combines multiple transformations, thereby minimizing the amount of
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+ This script computes the transforms needed to align EPI and
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+ anatomical datasets using a cost function designed for this purpose. The
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+ script combines multiple transformations, thereby minimizing the amount of
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interpolation applied to the data.
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-
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+
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Basic Usage:
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align_epi_anat.py -anat anat+orig -epi epi+orig -epi_base 5
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-
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+
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The user must provide EPI and anatomical datasets and specify the EPI
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- sub-brick to use as a base in the alignment.
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+ sub-brick to use as a base in the alignment.
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Internally, the script always aligns the anatomical to the EPI dataset,
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- and the resulting transformation is saved to a 1D file.
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- As a user option, the inverse of this transformation may be applied to the
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+ and the resulting transformation is saved to a 1D file.
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+ As a user option, the inverse of this transformation may be applied to the
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EPI dataset in order to align it to the anatomical data instead.
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This program generates several kinds of output in the form of datasets
@@ -182,7 +182,7 @@ def _list_outputs(self):
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epi_prefix = '' .join (self ._gen_fname (self .inputs .in_file ).split ('+' )[:- 1 ])
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outputtype = self .inputs .outputtype
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if outputtype == 'AFNI' :
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- ext = '.HEAD'
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+ ext = '.HEAD'
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else :
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Info .output_type_to_ext (outputtype )
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matext = '.1D'
@@ -620,7 +620,7 @@ class AutoTLRCInputSpec(CommandLineInputSpec):
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mandatory = True ,
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exists = True ,
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copyfile = False )
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- base = traits .Str (
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+ base = traits .Str (
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desc = ' Reference anatomical volume'
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' Usually this volume is in some standard space like'
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' TLRC or MNI space and with afni dataset view of'
@@ -706,7 +706,7 @@ def _list_outputs(self):
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ext = '.HEAD'
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outputs ['out_file' ] = os .path .abspath (self ._gen_fname (self .inputs .in_file , suffix = '+tlrc' )+ ext )
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return outputs
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-
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+
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class BandpassInputSpec (AFNICommandInputSpec ):
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in_file = File (
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desc = 'input file to 3dBandpass' ,
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