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sty: break lines in desc, do not escape quote marks [skip ci]
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nipype/interfaces/afni/preprocess.py

Lines changed: 33 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -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
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.
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* 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 ...""")
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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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