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Added options for mrtrix_track_roi2roi parameters, that allow setting FA threshold, curvature threshold and length threshold #113

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Added options for mrtrix_track_roi2roi parameters, that allow setting FA threshold, curvature threshold and length threshold #113

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56 changes: 51 additions & 5 deletions external/mrtrix/mrtrix_track_roi2roi.m
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
function [pdb_file, status, results] = mrtrix_track_roi2roi(files, roi1, roi2, seed, mask, mode, n, n_max, bkgrnd, verbose)

function [pdb_file, status, results] = mrtrix_track_roi2roi(files, roi1, roi2, seed, mask, mode, n, n_max, bkgrnd, verbose, varargin)
% ,fiber_length,fa_th,fa_th_init,curv_th,
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I don't think you want this line to be here

% Provided a csd estimate, generate estimates of the fibers starting in the
% seed region, touching both roi1 and roi2.
%
Expand All @@ -19,7 +19,13 @@
% defaults (which is 100 x n).
% bkgrnd: on unix, whether to perform the operation in another process
% verbose: whether to display stdout to the command window.
%
%
% the next parameters are optional, if not added or empty [], the default is used:
% fiber_length: maximum fiber length, if not added, set to 200 as in mrtrix default.
% fa_th: fa threshold, if not added, set to .1 as in mrtrix default.
% fa_th_init: fa initiation threshold, if not added, set to .2 as in mrtrix default.
% curv_th: curvature threshold, if not added, set to 1 or 2 as in mrtrix default.
%
% Franco, Bob & Ariel (c) Vistalab Stanford University 2013

if notDefined('verbose'),verbose = true; end
Expand All @@ -38,15 +44,55 @@
error('Input "%s" is not a valid tracking mode', mode);
end

% define mrtrix default parameters:
fiber_length=200;
fa_th=.1;
fa_th_init=2*.1;
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Is there any particular intention with writing 0.2 as 2 * .1? I had to read this a couple of times to understand what this is supposed to be

switch mode_str
case {'SD_PROB'}
curv_th=2;
case {'SD_STREAM','DT_STREAM'}
curv_th=1;
end
% change mrtrix default if there is an entry:
if ~isempty(varargin)
if length(varargin)>=1
if ~isempty(varargin{1})
fiber_length=varargin{1};
end
end
if length(varargin)>=2
if ~isempty(varargin{2}),
fa_th=varargin{2};
end
end
if length(varargin)>=3
if ~isempty(varargin{3}),
fa_th_init=varargin{3};
end
end
if length(varargin)>=4
if ~isempty(varargin{4})
curv_th=varargin{4};
end
end
end

% disp parameters
disp(['tracking parameters: fiber length=' int2str(fiber_length) ', fa th=' num2str(fa_th),...
', fa init th=' num2str(fa_th_init) ', curv th=' num2str(curv_th)])

% Track, using deterministic estimate:
tck_file = strcat(strip_ext(files.csd), '_' , strip_ext(roi1), '_', strip_ext(roi2), '_', ...
strip_ext(seed) , '_', strip_ext(mask), '_', mode, '.tck');

% Generate a UNIX command string.
switch mode_str
case {'SD_PROB', 'SD_STREAM'}
cmd_str = sprintf('streamtrack -seed %s -mask %s -include %s -include %s %s %s %s -number %d -maxnum %d -stop',...
seed,mask, roi1, roi2, mode_str, files.csd, tck_file, n, n_max);
cmd_str = sprintf(['streamtrack -seed %s -mask %s -include %s -include %s %s %s %s -number %d -maxnum %d -stop', ...
' -length %d -cutoff %g -initcutoff %g -curvature %d'],...
seed,mask, roi1, roi2, mode_str, files.csd, tck_file, n, n_max,...
fiber_length,fa_th,fa_th_init,curv_th);
% The following lines of code could be intergated here, to allow for
% tracking between ROIs using a tensor-based deterministic tractography
% case {'DT_STREAM'}
Expand Down