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 This program is for visualizing the volumetric output of tracking,
 mostly for the '-dump_rois ...' from 3dTrackID.  These are basically
 the WMC (white matter connection) maps through which tract bundles run
 (for DET and MINIP tracking modes), or through which a suprathreshold
 number of tracts run in PROB mode.

 This program creates surface-ized views of the separate WMCs which can
 be viewed simultaneously in 3D with SUMA.

  Ver. 1.4 (PA Taylor, Feb 12, 2019)



  fat_proc_connec_vis  \
    -in_rois       NETROIS       \
    -prefix        PPP           \
   {-prefix_file   FFF}          \
   {-tsmoo_kpb     KPB}          \
   {-tsmoo_niter   NITER}        \
   {-iso_opt       ISO_OPT}      \
   {-trackid_no_or}              \
   {-output_tcat}                \
   {-output_tstat}               \
   {-wdir          WWW}          \


    -in_rois NETROIS   :list of separate files, each with single ROI
                        volume mask; can include wildcards, etc. to specify
                        the list

    -prefix      PPP   :directory to contain the output files: *cmd.txt and
                        surface files such as *.gii and *.niml.dset; the
                        namebase of files within this directory will be the
                        default for the program, "wmc".  The value PPP
                        can contain parts of a path in it.
    -prefix_file FFF   :prefix for the output files: *cmd.txt and surface
                        files such as *.gii and *.niml.dset; can include
                        path steps; and can make one level of a new directory.
                        For example, if FFF were "A/B", then the program
                        could make a new directory called "A" if it didn't
                        exist already and populate it with individual files
                        having the same prefix "B".

    -tsmoo_kpb   KPB   :"KPB" parameter in IsoSurface program;  default
                        value is 0.01.
    -tsmoo_niter NITER :"NITER" parameter in IsoSurface program;  default
                        value is 6.
    -iso_opt   ISO_OPT :input one of the "iso* options" from IsoSurface
                        program, such as "isorois+dsets", "mergerois", etc.
                        Quotations around the entry may be needed, esp
                        if something like the "-mergerois [LAB_OUT]" route
                        is being followed.
                        Default: isorois+dsets

    -trackid_no_or     :use this option to have the program recognize the
                        naming convention of 3dTrackID output and to ignore
                        the OR-logic ROIs, including only the AND-logic (AKA
                        pairwise) connections.  This is mainly useful when
                        wildcard expressions are using for '-in_rois NETROIS'.

    -output_tcat       :flag to output the multibrick file of concatenated
                        ROI masks; note that the [0]th brick will be all
                        zeros (it is just a place holder).  So, if there are
                        N ROI maps concatenated, there will be N+1 bricks
                        in the output dset, which has name PPP_tcat.nii.gz.
    -output_tstat      :flag to output the single brick file from the 3dTstat
                        operation on the tcat dset.  If there were N ROI maps
                        concatenated, then the largest value should be N.
                        The output file's name will be PPP_tstat.nii.gz.

    -wdir    WWW       :"__WDIR_connec_vis_PPP", where PPP is the input
    -no_clean          :is an optional switch to NOT remove working
                        directory WWW; (default: remove working dir).

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    fat_proc_connec_vis \
        -in_rois o.prob/NET*       \
        -prefix surf_prob          \

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