Usage 1: A script to transform an antomical dataset to align with
         some standard space template.

   @auto_tlrc [options] <-base template> <-input anat>
   Mandatory parameters:
      -base template :  Reference anatomical volume
                        Usually this volume is in some standard space like
                        TLRC or MNI space and with afni dataset view of
                        Preferably, this reference volume should have had
                        the skull removed but that is not mandatory.
                        AFNI's distribution contains several templates.
                        For a longer list, use "whereami -show_templates"
          TT_N27+tlrc --> Single subject, skull stripped volume.
                       This volume is also known as
                       N27_SurfVol_NoSkull+tlrc elsewhere in
                       AFNI and SUMA land.
                       (www.loni.ucla.edu, www.bic.mni.mcgill.ca)
                       This template has a full set of FreeSurfer
                       surface models that can be used in SUMA.
                       For details, see Talairach-related link:
          TT_icbm452+tlrc --> Average volume of 452 normal brains.
                           Skull Stripped. (www.loni.ucla.edu)
          TT_avg152T1+tlrc --> Average volume of 152 normal brains.
                           Skull Stripped.(www.bic.mni.mcgill.ca)
          TT_EPI+tlrc --> EPI template from spm2, masked as TT_avg152T1
                          TT_avg152 and TT_EPI volume sources are from
                          SPM's distribution. (www.fil.ion.ucl.ac.uk/spm/)

          If you do not specify a path for the template, the script
          will attempt to locate the template AFNI's binaries directory.

          NOTE: These datasets have been slightly modified from
                their original size to match the standard TLRC
                dimensions (Jean Talairach and Pierre Tournoux
                Co-Planar Stereotaxic Atlas of the Human Brain
                Thieme Medical Publishers, New York, 1988).
                That was done for internal consistency in AFNI.
                You may use the original form of these
                volumes if you choose but your TLRC coordinates
                will not be consistent with AFNI's TLRC database
                (San Antonio Talairach Daemon database), for example.
      -input anat    :  Original anatomical volume (+orig).
                        The skull is removed by this script
                        unless instructed otherwise (-no_ss).
   Optional parameters:
      -no_ss         :  Do not strip skull of input data set
                        (because skull has already been removed
                        or because template still has the skull)
      NOTE: The -no_ss option is not all that optional.
         Here is a table of when you should and should not use -no_ss

                        Template          Template
                        WITH skull        WITHOUT skull
         WITH skull      -no_ss            xxx

         WITHOUT skull   No Cigar          -no_ss

         Template means: Your template of choice
         Dset. means: Your anatomical dataset
         -no_ss means: Skull stripping should not be attempted on Dset
         xxx means: Don't put anything, the script will strip Dset
         No Cigar mean: Don't try that combination, it makes no sense.

      -warp_orig_vol: Produce a TLRC version of the input volume, rather
                      than a TLRC version of the skull-stripped input.
                      This option is useful if you want the skull to be
                      preserved in the +tlrc output.
                      The default is to produce the skull-stripped version
                      of the input in +tlrc space.
      -dxyz MM          : Cubic voxel size of output DSET in TLRC
                          space. Default is the resolution of the
                          template. If you do not want your output
                          voxels to be cubic, then use the
                          -dx, -dy, -dz options below.
      -dx MX            : Size of voxel in the x direction
                          (Right-Left). Default is 1mm.
      -dy MY            : Size of voxel in the y direction
                          (Anterior-Posterior). Default is 1mm.
      -dz MZ            : Size of voxel in the z direction.
                          (Inferior-Superior). Default is 1mm.
      -pad_base  MM  :  Pad the base dset by MM mm in each directions.
                        That is needed to  make sure that datasets
                        requiring wild rotations do not get cropped.
                        Default is MM = 15.
                        If your output dataset is clipped, try increasing
                        MM to 25.000000 or
                        If that does not help, make sure
                        that the skull-stripped volume has no clipping.
                        If it does, then the skull stripping needs to
                        be corrected. Feel free to report such instances
                        to the script's authors.
      -keep_tmp      :  Keep temporary files.
      -clean         :  Clean all temp files, likely left from -keep_tmp
                        option then exit.
      -xform  XFORM  : Transform to use for warping:
                       Choose from affine_general or shift_rotate_scale
                       Default is affine_general but the script will
                       automatically try to use shift_rotate_scale
                       if the alignment does not converge.
      -no_avoid_eyes : An option that gets passed to 3dSkullStrip.
                       Use it when parts of the frontal lobes get clipped
                       See 3dSkullStrip -help for more details.
      -ncr           : 3dWarpDrive option -coarserot is now a default.
                       It will cause no harm, only good shall come of it.
                       -ncr is there however, should you choose NOT TO
                       want coarserot used for some reason
      -onepass       : Turns off -twopass option for 3dWarpDrive. This will
                       speed up the registration but it might fail if the
                       datasets are far apart.
      -twopass       : Opposite of -onepass, default.
      -maxite NITER  : Maximum number of iterations for 3dWarpDrive.
                       Note that the script will try to increase the
                       number of iterations if needed.
                       When the maximum number of iterations is reached
                       without meeting the convergence criteria,
                       the script will double the number of iterations
                       and try again. If the second pass still fails,
                       the script will continue unless the user specifies the
                       -not_OK_maxite option.
                       The default number of iterations is 50 for first
                       pass and then doubled to 100 in second pass.
                       To reset to former default, set maxite to 0
      -not_OK_maxite : See -maxite option.
      -inweight      : Apply -weight INPUT (in 3dWarpDrive).
                       By default, 3dWarpDrive uses the BASE dataset to
                       weight the alignment cost.  Use this option to
                       weight via the INPUT dataset, instead.
                       This might be useful for partial coverage cases.
      -rigid_equiv   : Also output a the rigid-body version of the
                       alignment. This would align the brain with
                       TLRC axis without any distortion. Note that
                       the resultant .Xrigid volume is NOT in TLRC
                       space. Do not use this option if you do not
                       know what to do with it!
                       For more information on how the rigid-body
                       equivalent transformation is obtained, see
                       cat_matvec -help 's output for the -P option.
      -init_xform XFORM0.1D: Apply affine transform in XFORM0.1D before
                       beginning registration and then include XFORM0.1D
                       in the final xform.
                       To verify that XFORM0.1D does what you think
                       it should be doing, try:
                 3dWarp    -matvec_out2in XFORM0.1D \
                           -prefix pre.anat anat+orig
                       and verify that 'pre.anat+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
                    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.

          Note: You can also use -init_xform AUTO_CENTER to automatically
                run @Align_Centers if the centers are off by more than
                40 mm.
                AUTO_CENTER_CM would do the centering based on the
                center of mass rather than the center of the volume grids.

                You can force centering with -init_xform CENTER
                or with -init_xform CENTER_CM regardless of the center
                distance between volumes

      -no_pre: Delete temporary dataset created by -init_xform

      -out_space spacename: Set output to a particular space
                       Usually, output space is determined by the space
                       of the input template and does not need to be set
                       explicitly here

      -3dAllineate: Use 3dAllineate with the lpa+ZZ cost function
                    instead of 3dWarpDrive
      -3dAlcost costfunction : use another cost function, like nmi,
                    for instance
      -overwrite: Overwrite existing output.
                  With this option, 3dSkullstrip will get rerun even
                  if skull stripped volume is found on disk, unless of
                  course you use the -no_ss option.
                  This option has not been fully tested under the myriad
                  combinations possible. So check closely the first
                  time you use it, if use it you must

Note on the subject of transforms:
   The script will output the final transform in a 1D file with the
   extension Xat.1D, say THAT_NAME.1D
   Call this transform Mt and let Xt and Xo be the 4x1 column vectors
   coordinates of the same voxel in standard (t) and original (o)
   space, respectively. The transform is such that Xo = Mt Xt
   You can use this transform to manually warp a volume in orig
   space to the standard space with:

      3dWarp -matvec_out2in THAT_NAME.Xat.1D -prefix PPP SOME_VOL+orig.
      3drefit -view +tlrc PPP+orig

   @auto_tlrc -base TT_N27+tlrc. -input SubjectHighRes+orig.
    (the output is named SubjectHighRes+TLRC, by default.
     See -suffix for more info.)

Usage 2: A script to transform any dataset by the same TLRC
         transform obtained with @auto_tlrc in Usage 1 mode

         Note: You can now also use adwarp instead.

   @auto_tlrc [options] <-apar TLRC_parent> <-input DSET>
   Mandatory parameters:
      -apar TLRC_parent : An anatomical dataset in tlrc space
                          created using Usage 1 of @auto_tlrc
                          From the example for usage 1, TLRC_parent
                          would be: SubjectHighRes+TLRC
      -input DSET       : Dataset (typically EPI time series or
                          statistical datset) to transform to
                          tlrc space per the xform in TLRC_parent
      -dxyz MM          : Cubic voxel size of output DSET in TLRC
                          space Default MM is 1. If you do not
                          want your output voxels to be cubic
                          Then use the -dx, -dy, -dz options below.
      -dx MX            : Size of voxel in the x direction
                          (Right-Left). Default is 1mm.
      -dy MY            : Size of voxel in the y direction
                          (Anterior-Posterior). Default is 1mm.
      -dz MZ            : Size of voxel in the z direction.
                          (Inferior-Superior).Default is 1mm.
   Optional parameters:
      -pad_input  MM    :  Pad the input DSET by MM mm in each direction.
                        That is needed to  make sure that datasets
                        requiring wild rotations do not get cropped.
                        Default is MM = 15.
                        If your output dataset is clipped, try increasing
                        MM to 25.000000 or
                        If that does not help, report the
                        problem to the script's authors.
      -onewarp          : Create follower data (-apar use) with one interpolation
                          step, instead of two. - Now default
                          This option reduces blurring of the output data.
      -twowarp          : Create follower data (-apar use) with two interpolations
                          step, instead of one.
                          This option is for backward compatibility.

   @auto_tlrc  -apar SubjectHighRes+tlrc. \
                  -input Subject_EPI+orig. -dxyz 3
    (the output is named Subject_EPI_at+TLRC, by default.

Common Optional parameters:
   -rmode     MODE:  Resampling mode. Choose from:
                     linear, cubic, NN or quintic .
                     Default for 'Usage 1' is cubic.
                     Default for 'Usage 2' is cubic for 3dWarp,
                      followed by Bk for the 3dresample step.
   -prefix   prefix: Name output dataset
                     (xxx -> xxx+tlrc, yyy.nii.gz, zzz.nii)
   -suffix    SUF :  Name the output dataset by append SUF
                     to the prefix of the input data for the output.
                     Default for SUF is NONE (see below)
              NOTE:  You can now set SUF to 'none' or 'NONE' and enable
                     afni's warp on demand features.
                     With NIFTI input volumes -suffix defaults to _at
   -keep_view     :  Do not mark output dataset as +tlrc
   -base_copy COPY_PREFIX: Copy base (template) dataset into COPY_PREFIX.
                           You can use ./ for COPY_PREFIX if you
                           want the copy to have the same name as the
   -base_list     : List the full path of the base dataset
   -verb          :  Yakiti yak yak

When you're down and troubled and you need a helping hand:
   1- Oh my God! The brain is horribly distorted (by Jason Stein):
      The probable cause is a failure of 3dWarpDrive to converge.
      In that case, rerun the script with the option
      -xform shift_rotate_scale. That usually takes care of it.
      The script now has a mechanism for detecting cases
      where convergence is not reached and it will automatically
      change -xform to fix the problem. So you should see very
      few such cases. If you do, check the skull stripping
      step for major errors and if none are found send the
      authors a copy of the command you used, the input and base
      data and they'll look into it.
   2- Parts of the frontal cortex are clipped in the output:
      That is likely caused by aggressive skull stripping.
      When that happens, use the -no_avoid_eyes option.
   3- Other parts of the brain are missing:
      Examine the skull stripped version of the brain
      If the source of the problem is with the stripping,
      then you'll need to run 3dSkullStrip manually and
      select the proper options for that dataset.
      Once you have a satisfactorily stripped brain, use that
      version as input to @auto_tlrc along with the -no_ss option.
   4- Skull stripped dataset looks OK, but TLRC output is clipped.
      Increase the padding from the default value by little more
      than the size of the clipping observed. (see -pad_*
      options above)
   5- The high-res anatomical ends up at a lower resolution:
      That is because your template is at a lower resolution.
      To preserve (or control) the resolution of your input,
      run @auto_tlrc in usage 2 mode and set the resolution
      of the output with the -d* options.
   6- I want the skulled anatomical, not just the stripped
      anatomical in TLRC space:
      Use @auto_tlrc in usage 2 mode.
   7- What if I want to warp EPI data directly into TLRC space?
      If you have an EPI template in TLRC space you can use it
      as the base in @auto_tlrc, usage 1 mode. You can use whatever
      you want as a template. Just make sure you are warping
      apples to oranges, not apples to bananas for example.
   8- Bad alignment still:
      Check that the center of your input data set is not too
      far off from that of the template. Centers (not origins)
      of the templates we have are close to 0, 0, 0. If your
      input dataset is 100s of mm off center then the alignment
      will fail.
      The easiest way around this is to add -init_xform AUTO_CENTER
      to your command. If that still fails you can try to manually
      shift all of the input data in your session by an equal amount
      to get the centers closer to zero.
      For example, say the center of your subject's volumes
      is around 100, 100, 100. To shift the centers close to 0, 0, 0 do:
      3drefit -dxorigin -100 -dyorigin -100 -dzorigin -100 Data+orig
      Then use @auto_tlrc on the shifted datasets.
      Take care not to shift datasets from the same session by differing
      amounts as they will no longer be in alignment.

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. Seach is approximate.

Written by Ziad S. Saad (saadz@mail.nih.gov)