@@ -3088,39 +3088,39 @@ class QwarpInputSpec(AFNICommandInputSpec):
30883088 name_template = 'ppp_%s' ,
30893089 name_source = ['in_file' ],
30903090 desc = """\
3091- Sets the prefix/suffix for the output datasets. \
3092- * The source dataset is warped to match the base \
3093- and gets prefix 'ppp'. (Except if '-plusminus' is used.)
3094- * The final interpolation to this output dataset is \
3095- done using the \ ' wsinc5\ ' method. See the output of \
3096- 3dAllineate -HELP \
3097- (in the "Modifying \ ' -final wsinc5\ ' " section) for \
3098- the lengthy technical details. \
3099- * The 3D warp used is saved in a dataset with \
3100- prefix \ ' ppp_WARP\ ' -- this dataset can be used \
3101- with 3dNwarpApply and 3dNwarpCat, for example. \
3102- * To be clear, this is the warp from source dataset \
3103- coordinates to base dataset coordinates, where the \
3104- values at each base grid point are the xyz displacments \
3105- needed to move that grid point\ ' s xyz values to the \
3106- corresponding xyz values in the source dataset: \
3107- base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z) \
3108- Another way to think of this warp is that it \ ' pulls\' \
3109- values back from source space to base space. \
3110- * 3dNwarpApply would use \ ' ppp_WARP\ ' to transform datasets \
3111- aligned with the source dataset to be aligned with the \
3112- base dataset. \
3113- ** If you do NOT want this warp saved, use the option \ ' -nowarp\' . \
3114- -->> (However, this warp is usually the most valuable possible output!) \
3115- * If you want to calculate and save the inverse 3D warp, \
3116- use the option \ ' -iwarp\ ' . This inverse warp will then be \
3117- saved in a dataset with prefix \ ' ppp_WARPINV\' . \
3118- * This inverse warp could be used to transform data from base \
3119- space to source space, if you need to do such an operation. \
3120- * You can easily compute the inverse later, say by a command like \
3121- 3dNwarpCat -prefix Z_WARPINV \ ' INV(Z_WARP+tlrc)\' \
3122- or the inverse can be computed as needed in 3dNwarpApply, like \
3123- 3dNwarpApply -nwarp \ ' INV(Z_WARP+tlrc)\ ' -source Dataset.nii ...""" )
3091+ Sets the prefix/suffix for the output datasets.
3092+ * The source dataset is warped to match the base
3093+ and gets prefix 'ppp'. (Except if '-plusminus' is used
3094+ * The final interpolation to this output dataset is
3095+ done using the 'wsinc5' method. See the output of
3096+ 3dAllineate -HELP
3097+ (in the "Modifying '-final wsinc5'" section) for
3098+ the lengthy technical details.
3099+ * The 3D warp used is saved in a dataset with
3100+ prefix 'ppp_WARP' -- this dataset can be used
3101+ with 3dNwarpApply and 3dNwarpCat, for example.
3102+ * To be clear, this is the warp from source dataset
3103+ coordinates to base dataset coordinates, where the
3104+ values at each base grid point are the xyz displacments
3105+ needed to move that grid point's xyz values to the
3106+ corresponding xyz values in the source dataset:
3107+ base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z)
3108+ Another way to think of this warp is that it 'pulls'
3109+ values back from source space to base space.
3110+ * 3dNwarpApply would use 'ppp_WARP' to transform datasets
3111+ aligned with the source dataset to be aligned with the
3112+ base dataset.
3113+ ** If you do NOT want this warp saved, use the option '-nowarp'.
3114+ -->> (However, this warp is usually the most valuable possible output!)
3115+ * If you want to calculate and save the inverse 3D warp,
3116+ use the option '-iwarp'. This inverse warp will then be
3117+ saved in a dataset with prefix 'ppp_WARPINV'.
3118+ * This inverse warp could be used to transform data from base
3119+ space to source space, if you need to do such an operation.
3120+ * You can easily compute the inverse later, say by a command like
3121+ 3dNwarpCat -prefix Z_WARPINV 'INV(Z_WARP+tlrc)'
3122+ or the inverse can be computed as needed in 3dNwarpApply, like
3123+ 3dNwarpApply -nwarp 'INV(Z_WARP+tlrc)' -source Dataset.nii ...""" )
31243124 resample = traits .Bool (
31253125 desc = 'This option simply resamples the source dataset to match the'
31263126 'base dataset grid. You can use this if the two datasets'
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