:orphan: .. _ahelp_@align_partial_oblique: ********************** @align_partial_oblique ********************** .. contents:: :local: | .. code-block:: none Parsing ... Usage 1: A script to align a full coverage T1 weighted non-oblique dataset to match a partial coverage T1 weighted non-oblique dataset Alignment is done with a rotation and shift (6 parameters) transform only. Script is still in testing phase @align_partial_oblique [options] <-base FullCoverageT1> <-input PartialCoverageObliqueT1> Mandatory parameters: -base FullCoverageT1: Reference anatomical full coverage volume. -input PartialCoverageObliqueT1: The name says it all. Optional parameters: -suffix SUF : Output dataset name is formed by adding SUF to the prefix of the base dataset. The default suffix is _alnd_PartialCoverageObliqueT1 -keep_tmp : Keep temporary files. -clean : Clean all temp files, likely left from -keep_tmp option then exit. -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. Example: @align_partial_oblique -base ah_SurfVol+orig. -input ah_T1W_anat+orig. Written by Ziad S. Saad, for Ikuko (saadz@mail.nih.gov) SSCC/NIMH/NIH/DHHS