@SUMA_AlignToExperiment                                                 \
    <-exp_anat Experiment_Anatomy> <-surf_anat Surface_Anatomy>         \
    [dxyz] [-wd] [-prefix PREFIX]                                       \
    [-EA_clip_below CLP] [-align_centers] [-ok_change_view]             \
    [-strip_skull WHICH]

Creates a version of Surface Anatomy that is registered to Experiment

Mandatory parameters:

    <-exp_anat Experiment_Anatomy>
        Name of high resolution anatomical data set in register with
        experimental data.

    <-surf_anat Surface_Anatomy>
        Path and name of high resolution antomical data set used to
        create the surface.

  NOTE: In the old usage, there were no -exp_anat and -surf_anat flags
  and the two volumes had to appear first on the command line and in
  the proper order.

Optional parameters:

   [-dxyz DXYZ]: This optional parameter indicates that the anatomical
                volumes must be downsampled to dxyz mm voxel
                resolution before registration. That is only necessary
                if 3dvolreg runs out of memory.  You MUST have
                3dvolreg that comes with afni distributions newer than
                version 2.45l. It contains an option for reducing
                memory usage and thus allow the registration of large
                data sets.

   [-out_dxyz DXYZ]: Output the final aligned volume at a cubic
                voxelsize of DXYZmm. The default is based on the grid
                of ExpVol.

   [-wd]: Use 3dWarpDrive's general affine transform (12 param)
                instead of 3dvolreg's 6 parameters.  If the anatomical
                coverage differs markedly between 'Experiment Anatomy'
                and 'Surface Anatomy', you might need to use
                -EA_clip_below option or you could end up with a very
                distorted brain.  The default now is to use -coarserot
                option with 3dWarpDrive, this should make the program
                more robust. If you want to try running without it the
                add -ncr with -wd I would be interested in examining
                cases where -wd option failed to produce a good

   [-al]: Use 3dAllineate to do the 12 parameter alignment. Cost
                function is 'lpa'.

   [-al_opt 'Options for 3dAllineate']: Specify set of options between
                quotes to pass to 3dAllineate.

   [-ok_change_view]: Be quiet when view of registered volume is
                changed to match that of the Experiment_Anatomy, even
                when rigid body registration is used.

   [-strip_skull WHICH]: Use 3dSkullStrip to remove non-brain tissue
                and potentially improve the alignment. WHICH can be
                one of 'exp_anat', 'surf_anat', 'both', or 'neither'
                (default).  In the first case, the skull is removed
                from Experiment_Anatomy dataset, in the second it is
                removed from the surf_anat dataset.  With 'both' the
                skull is removed from Experiment_Anatomy and

   [-skull_strip_opt 'Options For 3dSkullStrip']: Pass the options
                between quotes to 3dSkullStrip.

   [-align_centers]: Adds an additional transformation to align the
                volume centers. This is a good option to use when
                volumes are severely out of alignment.

   [-init_xform XFORM0.1D]: Apply affine transform in XFORM0.1D to
                Surface_Anatomy before beginning registration.  After
                convergence, combine XFORM.1D and the the registration
                matrix to create the output volume To verify that
                XFORM0.1D does what you think it should be doing, try:
                    3dWarp -matvec_out2in XFORM0.1D           \
                           -prefix pre.SurfVol SurfVol+orig
                and verify that 'pre.SurfVol+orig' is transformed by
                XFORM0.1D as you expected it to be.
                XFORM0.1D can be obtained in a variety of ways. One
                of which involves extracting it from a transformed
                volume.  For example, say you want to perform an
                initial rotation that is equivalent to:
                    3drotate -matvec_order RotMat.1D          \
                          -prefix struct.r struct+orig
                The equivalent XFORM0.1D is obtained with:
                    cat_matvec 'struct.r+orig::ROTATE_MATVEC_000000' -I  \
                           > XFORM0.1D
                See cat_matvec -help for more details on extracting
                appropriate affine transforms from dataset headers.
                See also Example 4 below.

   [-EA_clip_below CLP]: Set slices below CLPmm in 'Experiment
                Anatomy' to zero.  Use this if the coverage of
                'Experiment Anatomy' dataset extends far below the
                data in 'Surface Anatomy' dataset.  To get the value
                of CLP, use AFNI to locate the slice below which you
                want to clip and set CLP to the z coordinate from
                AFNI's top left corner. Coordinate must be in RAI,

   [-prefix PREFIX]: Use PREFIX for the output volume. Default is the

   [-surf_anat_followers Fdset1 Fdset2 ...]: Apply the same alignment
                transform to datasets Fdset1, Fdset2, etc.  This must
                be the last option on the command line.  All
                parameters following it are considered datasets.  You
                can transform other follower dsets manually by
                    3dAllineate -master Experiment_Anatomy              \
                        -1Dmatrix_apply Surface_Anatomy_Alnd_Exp.A2E.1D \
                        -input Fdset                                    \
                        -prefix Fdset_Alnd_Exp+orig                     \
                        -final NN

   [-followers_interp KERNEL]: Set the interpolation mode for the
                follower datasets. Default is NN, which is appropriate
                for ROI datasets.  Allowed KERNEL values are: NN,
                linear, cubic, or quintic
                Note: For atlas datasets, the KERNEL is forced to NN
                regardless of what you set here.
        of the 'Surface Anatomy' suffixed by _Alnd_Exp.

   [-atlas_followers]: Automatically set the followers to be atlases
                in the directory of -surf_anat. This way all the
                parcellations will get aligned to the experiment.

   [-echo]: Echo all commands to terminal for debugging

   [-keep_tmp]: Keep temporary files for debugging. Note that you
                should delete temporary files before rerunning the

   [-overwrite_resp RESP]: Answer 'overwrite' questions automatically.
                RESP (response) should be one of O/S/Q/A:
                    O : overwrite previous result
                    S : skip this step (applying previous result)
                    Q : quit the script
                    A : pause script and ask at each occurrence

NOTE: You must run the script from the directory where Experiment
Anatomy resides.

Example 1: For datasets with no relative distortion and comparable
           coverage.  Using 6 param. rigid body transform.
@SUMA_AlignToExperiment                                   \
    -exp_anat DemoSubj_spgrsa+orig.                       \
    -surf_anat ../FreeSurfer/SUMA/DemoSubj_SurfVol+orig.

Example 2: For datasets with some distortion and different coverage.
           Using 12 param. transform and clipping of areas below
@SUMA_AlignToExperiment                                      \
    -exp_anat ABanat+orig. -surf_anat DemoSubj_SurfVol+orig. \
    -wd -prefix DemoSubj_SurfVol_WD_Alnd_Exp                 \
    -EA_clip_below -30

Example 3: For two monkey T1 volumes with very different resolutions
           and severe shading artifacts.

@SUMA_AlignToExperiment                                      \
    -surf_anat MOanat+orig. -al                              \
    -exp_anat MoExpanat+orig.                                \
    -strip_skull both -skull_strip_opt -monkey               \
    -align_centers                                           \
    -out_dxyz 0.3

Example 4: When -exp_anat and -surf_anat have very different
           orientations Here is an egregious case where -exp_anat (EA)
           was rotated severely out of whack relative to -surf_anat
           (SV), AND volume centers were way off.  With the 'Nudge
           Dataset' plugin, it was determined that a 60deg.  rotation
           got SV oriented more like ExpAnat.  The plugin can be made
           to spit out an the 3dRotate command to apply the rotation:
                3drotate                                        \
                    -quintic -clipit                            \
                    -rotate 0.00I 60.00R 0.00A                  \
                    -ashift 0.00S 0.00L 0.00P                   \
                    -prefix ./SV_rotated+orig SV+orig
           We will get XFROM.1D from that rotated volume:
                cat_matvec 'SV_rotated+orig::ROTATE_MATVEC_000000' -I \
                    > XFORM0.1D
           and tell @SUMA_AlignToExperiment to apply both center
           alignment and XFORM0.1D
                @SUMA_AlignToExperiment                        \
                    -init_xform XFORM0.1D -align_centers       \
                    -surf_anat SV+orig  -exp_anat EA+orig      \
                    -prefix SV_A2E_autAUTPre
           Note 1: 'Nudge Dataset' can also be used to get the centers
           aligned, but that would be more buttons to press.
           Note 2: -init_xform does not need to be accurate, it is
           just meant to get -surf_anat to have a comparable

Global Help Options:

   -h_web: Open webpage with help for this program
   -hweb: Same as -h_web
   -h_view: Open -help output in a GUI editor
   -hview: Same as -hview
   -all_opts: List all of the options for this script
   -h_find WORD: Search for lines containing WORD in -help
                 output. Search is approximate.

More help may be found at:

Ziad Saad (saadz@mail.nih.gov)
SSCC/NIMH/ National Institutes of Health, Bethesda Maryland