Yeah - I'm happy to add that.


On Mon, Mar 31, 2014 at 2:45 PM, Satrajit Ghosh <notifications@github.com>wrote:

> In scripts/nipy_4d_realign:
>
> > +
> > +parser.add_argument('--slice_dim', type=int, metavar='Int', help="""Integer
> > +denoting the axis in `images` that is the slice axis.  In a 4D image, this will
> > +often be axis = 2 (default).""", default=2)
> > +
> > +parser.add_argument('--slice_dir', type=int, metavar='Int', help=""" 1 if the
> > +slices were acquired slice 0 first (default), slice -1 last, or -1 if acquire slice -1 first, slice 0 last.""", default=1)
> > +
> > +parser.add_argument('--apply', type=bool, metavar='Bool',
> > +                help="""Whether to apply the realignment and save output files (default), or just estimate the realignment parameters and save those in '.par' files. {True, False}. Default: True""", default=True)
> > +
> > +parser.add_argument('--make_figure', type=bool, metavar='Bool',
> > +                help="""Whether to generate a '.png' figure with the motion parameters across runs. {True, False}. Default: False """, default=False)
> > +
> > +parser.add_argument('--save_params', type=bool, metavar='Bool',
> > +                help="""Whether to save the motion corrections parameters (3 rotations, 3 translations). {True, False}. Default: False """, default=False)
>
> Perhaps this help should note:
> These rotations are not Euler angles, but a rotation vector. Please use
> nipyto_matrix44to convert to affine matrix.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/nipy/nipy/pull/265/files#r11138616>
> .
>