to match a template in TLRC space.
@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 (+tlrc). 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 (surfer.nmr.mgh.harvard.edu) surface models that can be used in SUMA. For details, see Talairach-related link: http://afni.nimh.nih.gov/afni/suma
- 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 skullDset. 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 = 40. If your output dataset is clipped, try increasing MM to 50.000000 or
60.000000.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 stop unless the user specifies the
-OK_maxite option.
-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+origand 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 volume. For example, say you want to perform an initial rotation that is equivalent to:
- 3drotate -matvec_order RotMat.1D
-prefix struct.r struct+origThe equivalent XFORM0.1D is obtained with:
- cat_matvec ‘struct.r+orig::ROTATE_MATVEC_000000’ -I
> XFORM0.1DSee 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 set explicitly here
- -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
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
Example: @auto_tlrc -base TT_N27+tlrc. -input SubjectHighRes+orig.
(the output is named SubjectHighRes+TLRC, by default.
See -suffix for more info.)
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 = 40. If your output dataset is clipped, try increasing MM to 50.000000 or
60.000000.If that does not help, report the problem to the script’s authors.
- -onewarp\ : Create follower data with one interpolation
- step, instead of two. This option reduces blurring of the output data. It is not used by default for backward compatibility.
Example: @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 Linear.
- Notice: Prior to 07/2010 -help output incorrecly stated
that rmode controlled interpolation in usage 1 and that it was ‘quintic’ by default. In fact, until this version, rmode did not affect ‘Usage 1’, and interpolation was linear Default for ‘Usage 2’ is quintic for 3dWarp,
followed by Bk for the 3dresample step.See option -onewarp for avoiding two interpolations
-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 template.
-base_list : List the full path of the base dataset
-verb : Yakiti yak yak
-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.