:orphan: .. _ahelp_3dLocalUnifize: ************** 3dLocalUnifize ************** .. contents:: :local: | OVERVIEW ======== .. code-block:: none This program takes an input and generates a simple "unifized" output volume. It estimates the median in the local neighborhood of each voxel, and uses that to scale each voxel's brightness. The result is a new dataset of brightness of order 1, which still has the interesting structure(s) present in the original. This program's output looks very useful to help with dataset alignment (esp. EPI-to-anatomical) in a wide array of cases. ver : 1.2 date : Jan 29, 2024 auth : PA Taylor (SSCC, NIMH, NIH) USAGE ===== .. code-block:: none This program is generally run as: 3dLocalUnifize [options] -prefix DSET_OUT -input DSET_IN where the following options exist: -input DSET_IN :(req) input dataset -prefix DSET_OUT :(req) output dataset name, including path -wdir_name WD :name of temporary working directory, which should not contain any path information---it will be created in the same directory as the final dataset is created (def: __wdir_LocalUni_, plus a random alphanumeric str) -echo :run this program very verbosely (def: don't do so) -no_clean :do not remove the working directory (def: remove it) ... and the following are 'tinkering' options, likely not needed in most cases: -local_rad LR :the spherical neighborhood's radius for the 3dLocalStat step (def: -3) -local_perc LP :the percentile used in the 3dLocalStat step, generating the scaling volume (def: 50) -local_mask LM :provide the masking option to be used in the 3dLocalStat step, which should be enclosed in quotes for passing along to the internal program call. So, to use a pre-existing mask, you might call this option like: -local_mask "-mask my_mask.nii.gz" To remove any masking, put the special keyword "None" as the option value. (def: "-automask") -filter_thr FT :put a ceiling on values in the final, scaled dataset, whose values should be of order 1; setting FT to be a value <=0 turns off this final filtering (def: 1.5) NOTES ===== .. code-block:: none This program is designed to not need a lot of tinkering with options, such as the '-local_* ..' ones. In most cases, the default scaling will be useful. EXAMPLES ======== .. code-block:: none 1. Basic local unifizing: 3dLocalUnifize \ -prefix vr_base_LU \ -input vr_base_min_outlier+orig.HEAD 1. Same as above, without masking: 3dLocalUnifize \ -prefix vr_base_LU_FOV \ -input vr_base_min_outlier+orig.HEAD \ -local_mask None