:orphan: .. _ahelp_fat_proc_align_anat_pair: ************************ fat_proc_align_anat_pair ************************ .. contents:: :local: | .. code-block:: none # ----------------------------------------------------------------------- This program is for aligning a T1w anatomical to a T2w anatomical using solid body parameters (i.e., only translation and rotation); this program does not clean or alter the T1w's brightness values (beyond minor smoothing from regridding). If one is going to be entering the T1w volume into the realms of FreeSurfer (FS), one might want to do this just *before* that step. If one wants axialized (or AC-PC-ized) anatomical volumes, one could perform that step on the T2w volume *before* using this function. This program mainly assumes that the T1w and T2w volume come from the same subject, and have similar contrasts expected for standard sequences and healthy adult brains. This might still work for other applications, but caveat emptor (even more than usual!). This would *not* be recommended for aligning brains that aren't from the same subject. As part of this alignment, the T1w volume will end up with the same orientation and a similar FOV as the T2w volume. Additionally, by default, the anatomical will be prepped a bit with an eye toward using FS, to have properties favorable to using it: + the T1w volume is resampled to isotropic spatial resolution of either 1 mm voxel edges or, if the input volume has any edge length smaller than this, to that value (i.e., resampled to 1 mm or the minimum input voxel edge length, whichever is less). The user can adjust this with the '-newgrid ...' option, or decide to match the grid of the T2w volume via '-out_t2w_grid'. + the T1w will have a FOV matching or quite similar to the T2w volume (as well as matching orientation). + [Aug 9, 2021] no longer checking about all even row dimensions---turned out not to be necessary. Note that, if you are preparing to use FS afterwards, then make sure to use their current help files, archives, etc. for all options and settings. For example, while at present (March, 2017) FS does seem to prefer isotropic voxels with 1 mm edge length by default, one can use high resolution options for data acquired at higher resolution. Anyways, you can read more about that there. Ver. 1.31 (PA Taylor, Sep 27, 2021) # ---------------------------------------------------------------------- OUTPUT: + NIFTI file: aligned T1w volume + QC snapshots of the T1w volume overlaying the T2w volume, and also the T1w edges overlaying the T2w volume. # ---------------------------------------------------------------------- RUNNING: fat_proc_align_anat_pair \ -in_t1w T1W \ -in_t2w T2W \ -prefix PPP \ {-newgrid RES} \ {-out_t2w_grid} \ {-in_t2w_mask MASK_T2W} \ {-do_ss_tmp_t1w} \ {-matrix MMM} \ {-workdir WWW} \ {-warp WAR} \ {-no_cmd_out} \ {-no_clean} where: -in_t1w T1W :T1w volume (required). -in_t2w T2W :T2w volume (required; preferably from same subject as T1W). -prefix PPP :output prefix for files and snapshots (required). -newgrid RES :specify output T1w volume's final resolution; will be isotropic in this value (default: 1 mm, or smallest voxel edge length of input T1W if that value is < 1 mm). -out_t2w_grid :final T1w volume is on the T2W volume's grid (with possible addition of padding with a slice of zeros if prepping for FS). -in_t2w_mask MASK_T2W :can input a mask to apply to the t2w volume for alignment purposes; might help in times of aligning hardship. -do_ss_tmp_t1w :during an intermediate step, apply skullstripping to the T1w volume-- final output is *not* skullstripped. This might be useful if there is lots of non-brain tissue still in the T1w volume. -warp WAR :can choose which of the possible affine degrees of freedom are employed in the warping, selecting them in the same manner described in 3dAllineate's help; that is, WAR can be any of shift_only, shift_rotate, shift_rotate_scale, or affine_general. Default: WAR = shift_rotate. -matrix MMM :one can apply a pre-made matrix that has been made by 3dAllineate previously. With this option. If you want. -workdir WWW :specify a working directory, which can be removed; (default name = '__WORKING_align_anat_pair') -no_cmd_out :don't save the command line call of this program and the location where it was run (otherwise, it is saved by default in the ODIR/). -no_clean :no not delete temporary working directory (default is to remove it to save disk space). # ---------------------------------------------------------------------- EXAMPLE # have isotropic 1x1x1 mm final anat: fat_proc_align_anat_pair \ -in_t1w MPRAGE.nii.gz \ -in_t2w T2w_anat.nii.gz \ -newgrid 1.0 \ -prefix t1w_alnd # match the final anat resolution to that of the t2w dset: fat_proc_align_anat_pair \ -in_t1w MPRAGE.nii.gz \ -in_t2w T2w_anat.nii.gz \ -out_t2w_grid \ -prefix t1w_alndb # -----------------------------------------------------------------------