asymm_report.csh

Overview

This is a script to compute volumes, surface areas, patch
surface areas and asymmetry ratios between
left and right regions from labeled datasets. These can be in a
native subject space or in a standard template space, as for an atlas.

Usage Example

asymm_report.csh                                 \
   -input HCA_lr_v0.9.nii.gz                     \
   -right_range 1 21                             \
   -left_range 31 51                             \
   -isosurf_dir ~/HCA_subjects/sub-101/surfs     \
   -isosurf_base HCA                             \
   -reportfile HCA_asymm_report.txt

Note only the input dset and the left and right ranges are *required*.

Options

-input input_dset    :required input dataset for relative region sizes

Provide index values either by range or by list files:
-right_range min max :minimum and maximum index values for right regions
-left_range  min max :minimum and maximum index values for left regions

with list files (columns or rows of numbers)
-right_list rightlist.1D : list of index values for right regions
-left_list  leftlist.1D : list of index values for left regions

-isosurf_dir dir      :directory with gifti surface files for regions
                       (default current directory)
-isosurf_base prefix  :beginning part of gifti file names shared across
                       regions
-make_isosurfs        :make isosurfaces from all regions in input volume
                       uses isosurf_dir for directory and isosurf_base for
                       prefix for output, e.g. isosurf_base.gii
-surf_patch           :compute areas of patches on surfaces
-surf_patch_surface surfdset :use one isosurface from labeled volume
                       for patches (different than isosurfaces for
                       individual regions)
-make_patch_surface   :generate new surface for patch area computations
-reportfile textout   :specify filename for text output (default is stdout)
-use_left_labels      :default is to use labels from right index regions in
                       output report. This option switches to use left labels
-surf_patch_prefix ppp:prefix for output labelled patch dset prefix.niml.dset
-surf_patch_smooth nn :neighborhood size for modal smoothing on surface
                       (2mm default). Check surface with smoothed data for
                       reasonableness
-method LI            :use method for comparison
                       LI (laterality index) = (L-R)/(L+R)
                       (negative values have right symmetry,
                        positive values have left symmetry
                        zero values are symmetric)
                       or
                       RL (right to left ratio) = R/L (Default)