@@ -3088,39 +3088,39 @@ class QwarpInputSpec(AFNICommandInputSpec):
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name_template = 'ppp_%s' ,
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name_source = ['in_file' ],
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desc = """\
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- Sets the prefix/suffix for the output datasets. \
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- * The source dataset is warped to match the base \
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- and gets prefix 'ppp'. (Except if '-plusminus' is used.)
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- * The final interpolation to this output dataset is \
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- done using the \ ' wsinc5\ ' method. See the output of \
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- 3dAllineate -HELP \
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- (in the "Modifying \ ' -final wsinc5\ ' " section) for \
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- the lengthy technical details. \
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- * The 3D warp used is saved in a dataset with \
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- prefix \ ' ppp_WARP\ ' -- this dataset can be used \
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- with 3dNwarpApply and 3dNwarpCat, for example. \
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- * To be clear, this is the warp from source dataset \
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- coordinates to base dataset coordinates, where the \
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- values at each base grid point are the xyz displacments \
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- needed to move that grid point\ ' s xyz values to the \
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- corresponding xyz values in the source dataset: \
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- base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z) \
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- Another way to think of this warp is that it \ ' pulls\' \
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- values back from source space to base space. \
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- * 3dNwarpApply would use \ ' ppp_WARP\ ' to transform datasets \
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- aligned with the source dataset to be aligned with the \
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- base dataset. \
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- ** If you do NOT want this warp saved, use the option \ ' -nowarp\' . \
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- -->> (However, this warp is usually the most valuable possible output!) \
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- * If you want to calculate and save the inverse 3D warp, \
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- use the option \ ' -iwarp\ ' . This inverse warp will then be \
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- saved in a dataset with prefix \ ' ppp_WARPINV\' . \
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- * This inverse warp could be used to transform data from base \
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- space to source space, if you need to do such an operation. \
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- * You can easily compute the inverse later, say by a command like \
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- 3dNwarpCat -prefix Z_WARPINV \ ' INV(Z_WARP+tlrc)\' \
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- or the inverse can be computed as needed in 3dNwarpApply, like \
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- 3dNwarpApply -nwarp \ ' INV(Z_WARP+tlrc)\ ' -source Dataset.nii ...""" )
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+ Sets the prefix/suffix for the output datasets.
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+ * The source dataset is warped to match the base
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+ and gets prefix 'ppp'. (Except if '-plusminus' is used
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+ * The final interpolation to this output dataset is
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+ done using the 'wsinc5' method. See the output of
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+ 3dAllineate -HELP
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+ (in the "Modifying '-final wsinc5'" section) for
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+ the lengthy technical details.
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+ * The 3D warp used is saved in a dataset with
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+ prefix 'ppp_WARP' -- this dataset can be used
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+ with 3dNwarpApply and 3dNwarpCat, for example.
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+ * To be clear, this is the warp from source dataset
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+ coordinates to base dataset coordinates, where the
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+ values at each base grid point are the xyz displacments
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+ needed to move that grid point's xyz values to the
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+ corresponding xyz values in the source dataset:
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+ base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z)
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+ Another way to think of this warp is that it 'pulls'
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+ values back from source space to base space.
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+ * 3dNwarpApply would use 'ppp_WARP' to transform datasets
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+ aligned with the source dataset to be aligned with the
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+ base dataset.
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+ ** If you do NOT want this warp saved, use the option '-nowarp'.
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+ -->> (However, this warp is usually the most valuable possible output!)
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+ * If you want to calculate and save the inverse 3D warp,
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+ use the option '-iwarp'. This inverse warp will then be
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+ saved in a dataset with prefix 'ppp_WARPINV'.
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+ * This inverse warp could be used to transform data from base
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+ space to source space, if you need to do such an operation.
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+ * You can easily compute the inverse later, say by a command like
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+ 3dNwarpCat -prefix Z_WARPINV 'INV(Z_WARP+tlrc)'
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+ or the inverse can be computed as needed in 3dNwarpApply, like
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+ 3dNwarpApply -nwarp 'INV(Z_WARP+tlrc)' -source Dataset.nii ...""" )
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resample = traits .Bool (
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desc = 'This option simply resamples the source dataset to match the'
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'base dataset grid. You can use this if the two datasets'
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