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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)
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RUNNING:
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} \
{-no_clean}
where
-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.
or
-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
prefix.
-no_clean :is an optional switch to NOT remove working
directory WWW; (default: remove working dir).
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EXAMPLE
fat_proc_connec_vis \
-in_rois o.prob/NET* \
-prefix surf_prob \
-trackid_no_or
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