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.. _ahelp_adjunct_suma_fs_roi_info:

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adjunct_suma_fs_roi_info
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OVERVIEW
========

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    In brief, this script is for quickly making some ROI stats (counts)
    for the SUMA/ directory created by @SUMA_Make_Spec_FS after running
    FreeSurfer's recon-all.  
    
    This program should be used *after* running adjunct_suma_fs_mask_and_qc,
    which makes a useful mask from the aparc+aseg dataset, called
    fs_parc_wb_mask.nii.gz.
    
    written by PA Taylor.
    
    # --------------------------------------------------------------------
    

USAGE
=====

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    This program has the following options:
    
        -sid          SUBJ_ID    :(req) subject ID
    
        -suma_dir     SUMA_DIR   :(req) SUMA/ directory output by AFNI's
                                  @SUMA_Make_Spec_FS
    
        -help                    :(opt) show help
    
        -hview                   :(opt) show help in text editor
    
        -ver                     :(opt) show version
    

OUTPUT
======

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    This script makes four *.1D files in the specified SUMA/ directory.
    Column labels are present in each file.  Note there are 2 ways to
    think of brain volumes after running FS's recon-all: the
    brainmask.nii* file (= br_mask), or the number of voxels in the full
    set of the aseg/aparc dset for a given atlas (= "all" segment, from
    the *_REN_all.nii* dset). 
    
        Nvox                    : number of voxels in the ROI, segment or 
                                  mask. This number is always an integer,
                                  >= 0.
    
        FR_BR_MASK              : fraction of the number of voxels, segment
                                  or mask, relative to the "br_mask" dset
                                  (that is, to the brainmask.nii* volume).
                                  
        FR_PARC_MASK            : fraction of the number of voxels, segment
                                  or mask, relative to the "parc_mask" dset
                                  (that is, to the fs_parc_wb_mask.nii.gz 
                                  volume that is created by the AFNI program
                                  adjunct_suma_fs_mask_and_qc).  If this file  
                                  does not exist, you will get a col of -1 
                                  values for the fraction;  but you *should* 
                                  just run adjunct_suma_fs_mask_and_qc.
    
                                  fs_parc_wb_mask.nii.gz is a filled in
                                  form of the aparc+aseg segmentation result.
    
        FR_ALL_ROI              : fraction of the number of voxels, segment
                                  or mask, relative to the full set of ROIs 
                                  in the given parcellation (that is, to the 
                                  *REN_all.nii* volume).
    
    Note that the ROI string labels are provided for each ROI, but behind
    a comment symbol in each line (so you can use them as regular *.1D
    files, with 1dcat, 1dtranspose, etc.).
    
      stats_fs_rois_2000_FT.1D  : info for the "2000" parcellation 
                                  (from the file: aparc+aseg_REN_all.nii*)
    
      stats_fs_rois_2009_FT.1D  : info for the "2009" parcellation 
                                  (from the file: aparc+aseg_REN_all.nii*)
    
      stats_fs_segs_2000_FT.1D  : info for the "2000" parc brain mask
                                  and tissue/segmentations (from the
                                  brainmask.nii* and aparc+aseg_REN_* files)
    
      stats_fs_segs_2009_FT.1D  : info for the "2009" parc brain mask
                                  and tissue/segmentations (from the
                                  brainmask.nii* and aparc.a2009s+aseg_REN_* 
                                  files)
    

EXAMPLE
=======

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      adjunct_suma_fs_roi_info                \
          -sid       sub-001                  \
          -suma_dir  group/sub-001/SUMA