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gen_mrtrix_track_roi2roi.m
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gen_mrtrix_track_roi2roi.m
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function [pdb_file, status, results] = gen_mrtrix_track_roi2roi(files, roi1, roi2, seed, mask, mode, n, n_max, cutoff, initcutoff, curvature, stepsize, bkgrnd, verbose)
% Provided a csd estimate, generate estimates of the fibers starting in the
% seed region, touching both roi1 and roi2.
%
% Parameters
% ----------
% files: structure, containing all the filenames generated with
% mrtrix_init.m.
% roi1: string, filename for a .mif format ROI file (mask).
% roi2: string, filename for a .mif format ROI file (mask).
% seed: string, filename for a .mif file contain part of the image in which
% to place the seeds.
% mask: string, filename for a .mif format of a mask.
% mode: Tracking mode: {'prob' | 'stream'} for probabilistic or
% deterministic tracking.
% n: The number of fibers to select.
% n_max: The number of fibers to generate, often need more than the
% 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.
%
% Franco, Bob & Ariel (c) Vistalab Stanford University 2013
if notDefined('verbose'),verbose = true; end
if notDefined('bkgrnd'), bkgrnd = false; end
if notDefined('clobber'), clobber = false;end
% Choose the tracking mode (probabilistic or stream)
switch mode
case {'prob','probabilistic','probabilistic tractography','p'}
mode_str = 'SD_PROB';
case {'stream','deterministic','deterministic tractography based on spherical deconvolution','d'}
mode_str = 'SD_STREAM';
case {'tensor','deterministic tractography based on a tensor model','t'}
mode_str = 'DT_STREAM';
otherwise
error('Input "%s" is not a valid tracking mode', mode);
end
% Construct filename with options
% Track, using deterministic estimate:
tck_file = strcat(strip_ext(files.csd), '_', strip_ext(roi1), '_', strip_ext(roi2), '_', ...
strip_ext(seed) , '_', strip_ext(mask), '_', ...
'cut',strrep(num2str(cutoff),'.',''), '_', ...
'initcut',strrep(num2str(initcutoff),'.',''), '_', ...
'curv',strrep(num2str(curvature),'.',''),'_', ...
'step',strrep(num2str(stepsize),'.',''), '_', ...
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 -minlength 10 -cutoff %d -initcutoff %d -curvature %d -step %d',...
seed, mask, roi1, roi2, mode_str, files.csd, tck_file, n, n_max, cutoff, initcutoff, curvature, stepsize);
%-cutoff value [0.075] set the FA or FOD amplitude cutoff for terminating tracks (default is 0.1). value the cutoff to use.
%-initcutoff value [0.075] set the minimum FA or FOD amplitude for initiating tracks (default is twice the normal cutoff).
% value the initial cutoff to use.
%-curvature radius [1, 0.5] set the minimum radius of curvature (default is 2 mm for DT_STREAM, 0 for SD_STREAM, 1 mm for SD_PROB and DT_PROB).
% radius the radius of curvature to use in mm.
% The following lines of code could be intergated here, to allow for
% tracking between ROIs using a tensor-based deterministic tractography
% case {'DT_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);
%
% [~, pathstr] = strip_ext(files.dwi);
% tck_file = fullfile(pathstr,strcat(strip_ext(files.dwi), '_' , strip_ext(roi), '_',...
% strip_ext(mask) , '_', mode, '-',num2str(nSeeds),'.tck'));
%
% % Generate the mrtrix-unix command.
% cmd_str = sprintf('streamtrack %s %s -seed %s -grad %s -mask %s -include %s -include %s %s -num %d', ...
% mode_str, files.dwi, roi, files.b, mask, roi1, roi2, tck_file, nSeeds);
otherwise
error('Input "%s" is not a valid tracking mode', mode_str);
end
% Launch the command
if ~(exist(tck_file,'file') ==2) || clobber == 1
[status, results] = mrtrix_cmd(cmd_str, bkgrnd, verbose);
else
fprintf('\nFound fiber tract file: %s.\n Loading it rather than retracking',tck_file)
status = 0;
results = 'loaded file from disk';
end
% Convert the tracks to pdb format:
pdb_file = strcat(strip_ext(tck_file), '.pdb');
mrtrix_tck2pdb(tck_file, pdb_file);
end
% Why does everything have to be so hard?
function no_ext = strip_ext(file_name)
[pathstr, no_ext, ext] = fileparts(file_name);
end