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.. _ahelp_compute_ROI_stats.tcsh:

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compute_ROI_stats.tcsh
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.. contents:: :local:


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.. code-block:: none

    
    ------------------------------------------------------------------------------
    compute_ROI_stats.tcsh  - compute per-ROI value statisics over a given dataset
    
       usage: compute_ROI_stats.tcsh [options] many_required_parameters...
    
       given:
          dset_ROI    : an ROI dataset
          dset_data   : a dataset to compute statistics over (e.g. TSNR)
          out_dir     : a directory to store the results in
          rset_label  : a label for dset_ROI
          rval_list   : a list of ROI values to compute stats over (e.g. 2 41 99)
    
       and maybe:
          stats_file  : name for the resulting statisics text file
    
       create a stats (text) file:
          create a depth map for dset_ROI
          for each requested ROI value rval in rval_list (for dset_ROI)
             compute and store in stats file:
                ROI          : ROI index value (rval)
    
                Nvox         : N voxels in dset_ROI rval region
                Nzer         : N ROI voxels that are zero in dset_data
                Dvox         : maximum ROI depth, in voxels (1.0 = 1 iso voxel)
                               = (max mm depth) / (iso voxel width)
    
                Tmin, T25%, Tmed, T75%, Tmax
                             : multiples of 25%-iles (with min/max)
    
                X, Y, Z      : x, y and z coordinates at max ROI depth
                               (coordinates are in DICOM/RAI orientation)
                ROI_name     : ROI label associated with ROI index (in dset_ROI)
    
    ------------------------------------------------------------------------------
    example 0: based on afni_proc.py
    
       compute_ROI_stats.tcsh                         \
           -out_dir    t.tsnr_stats_regress           \
           -dset_ROI   ROI_import_CAEZ_ML_resam+tlrc  \
           -dset_data  TSNR.FT+tlrc                   \
           -rset_label CAEZ_ML                        \
           -rval_list  4 41 99 999
    
    ------------------------------------------------------------------------------
    terminal options:
    
       -help                   : show this help
       -hist                   : show the revision history
       -ver                    : show the program version
    
    required parameters:
       -dset_ROI DSET_ROI      : ROI dataset containing regions of interest
                                 This dataset should (probably) contain the index
                                 values from -rval_list as regions of interest.
    
       -dset_data DSET_DATA    : volume to compute statistics over
                                 This dataset is for computing ROI statistics over,
                                 such as a TSNR volume.
    
       -out_dir OUT_DIR        : directory to put results into
                                 The output directory will hold a depth map for all
                                 DSET_ROI regions.
    
       -rset_label RSET_LABEL  : text label to refer to dset_ROI by
    
       -rval_list V1 V2 ...    : ROI index values (or ALL_LT)
                                 Each index with such voxels in DSET_ROI will be
                                 used to compute statistics from DSET_DATA.
    
                   example : -rval_list 2 41 99
                   example : -rval_list ALL_LT
    
    optional parameters:
     
       -make_html              : make addition table formatted with HTML-style
                                 warning coloring (for APQC HTML)
    
       -verb VERB              : specify verbosity level (3 == -echo)
                                 def: 1
       -echo                   : same as -verb 3
    
    ------------------------------------------------------------------------------
    R Reynolds Apr, 2021
    version version 1.7, March 8, 2024
    ------------------------------------------------------------------------------