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Add TractSeg/XTRACT DTI pipeline with JHU ANTs ROI export #4

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45 changes: 45 additions & 0 deletions examples/my_nodes/dp_node_ants_apply.m
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classdef dp_node_ants_apply < dp_node
% Wrapper around antsApplyTransforms onto a given reference grid
% input.nii_fn : image to be transformed (e.g. atlas labels in MNI)
% input.ref_fn : reference grid / output space (e.g. trimmed FA)
% input.affine_fn, input.invwarp_fn : from dp_node_ants_reg_quick
% output.nii_fn : resampled image in ref_fn space

properties
options = ''; % e.g. ' -n NearestNeighbor' for labels
use_inverse = 1; % default = inverse chain
end

methods

function obj = dp_node_ants_apply(options)
if (nargin>0), obj.options = options; end
obj.output_test = {'nii_fn'};
end

function output = i2o(obj, input)
output.nii_fn = dp.new_fn(input.op, input.nii_fn, '_ants');
output.ref_fn = input.ref_fn;
end

function output = execute(obj, input, output)
msf_mkdir(fileparts(output.nii_fn));
if obj.use_inverse
% apply inverse chain: template→subject (fixed → moving)
t = sprintf('-t "[%s,1]" -t "%s" ', input.affine_fn, input.invwarp_fn);
else
% apply forward chain: subject→template (moving → fixed)
t = sprintf('-t "%s" -t "%s" ', input.warp_fn, input.affine_fn);
end

if isempty(obj.options), obj.options = ' -n NearestNeighbor'; end

% cmd using composed transform chain "t" (forward or inverse, depending on use_inverse)
cmd = sprintf('antsApplyTransforms -d 3 -i "%s" -r "%s" %s -o "%s"%s', ...
input.nii_fn, input.ref_fn, t, output.nii_fn, obj.options);


system(cmd);
end
end
end
64 changes: 64 additions & 0 deletions examples/my_nodes/dp_node_ants_reg_quick.m
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classdef dp_node_ants_reg_quick < dp_node
% antsRegistrationSyN.sh (moving = input.nii_fn, fixed = input.target_fn)
% Outputs affine + forward/inverse warps in <input.op>

properties
options = ''; % include threads and preset here, e.g. ' ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=16 -t s'
end

methods

function obj = dp_node_ants_reg_quick(options)
if (nargin>0), obj.options = options; end
obj.output_test = {'affine_fn','warp_fn','invwarp_fn','warped_fn'};

end

function output = i2o(obj, input)
tmp = msf_fn_append(input.nii_fn, '_mni_');
prefix = msf_fn_new_path(input.op, tmp);
[pdir,pfx,~] = msf_fileparts(prefix);
prefix = fullfile(pdir, pfx); % ANTs prefix base (no ext)

output.prefix = prefix;
output.target_fn = input.target_fn;
output.affine_fn = [prefix '0GenericAffine.mat'];
output.warp_fn = [prefix '1Warp.nii.gz'];
output.invwarp_fn = [prefix '1InverseWarp.nii.gz'];
output.warped_fn = [prefix 'Warped.nii.gz']; % QC, remains in op
end


function output = execute(obj, input, output)
% set threads and build the command
thr = feature('numcores');
envp = sprintf('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=%d', thr);

% if user didn’t provide flags, default to symmetric registration (-t s)
if isempty(strtrim(obj.options))
flags = ' -t s';
else
flags = [' ' strtrim(obj.options)];
end

msf_mkdir(fileparts(output.warped_fn));


% full SyN variant
% cmd = sprintf('%s antsRegistrationSyN.sh -d 3 -f "%s" -m "%s" -o "%s"%s', ...
% envp, input.target_fn, input.nii_fn, output.prefix, flags);

% quick SyN variant
cmd = sprintf('%s antsRegistrationSyNQuick.sh -d 3 -f "%s" -m "%s" -o "%s"%s', ...
envp, input.target_fn, input.nii_fn, output.prefix, flags);


% Always save ANTs output to log in the same folder
log_fn = fullfile(fileparts(output.warped_fn), 'ants_registration.log');
cmd = [cmd, sprintf(' > "%s" 2>&1', log_fn)];

system(cmd);
end

end
end
53 changes: 53 additions & 0 deletions examples/my_nodes/dp_node_atlas_crop_to_mask.m
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classdef dp_node_atlas_crop_to_mask < dp_node
% Crop an atlas/label map with a provided mask (same grid).
%
% Inputs (from upstream):
% nii_fn - atlas / label image to crop (e.g. warped JHU labels)
% mask_fn - mask in the same space (e.g. trimmed FA brain mask)
% op - optional output directory
%
% Output:
% nii_fn - cropped atlas, saved as <op>/<basename>_crop.nii.gz

properties
suffix = '_crop';
end

methods
function obj = dp_node_atlas_crop_to_mask(suffix)
if nargin > 0
obj.suffix = suffix;
end
obj.output_test = {'nii_fn'};
end

function output = i2o(obj, input)
% Decide output folder
if isfield(input, 'op') && ~isempty(input.op)
op = input.op;
else
[op, ~, ~] = msf_fileparts(input.nii_fn);
end

% Use dp.new_fn to append suffix before extension
output.nii_fn = dp.new_fn(op, input.nii_fn, obj.suffix);
end

function output = execute(obj, input, output)
% Read atlas/labels and mask
[A, Ah] = mdm_nii_read(input.nii_fn);
B = mdm_nii_read(input.mask_fn);

% Basic safety
if ~isequal(size(A), size(B))
error('dp_node_atlas_crop_to_mask: atlas/mask size mismatch');
end

msf_mkdir(fileparts(output.nii_fn));

% Apply crop
mdm_nii_write(A .* (B > 0), output.nii_fn, Ah);

end
end
end
71 changes: 71 additions & 0 deletions examples/my_nodes/dp_node_segm_jhu.m
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classdef dp_node_segm_jhu < dp_node_segm

methods (Hidden)
function [labels, ids] = segm_info(obj)

% /usr/local/fsl/data/atlases/JHU-labels.xml

txt = { ...
'0: Unclassified', ... % Unclassified
'1: MCP', ... % Middle cerebellar peduncle
'2: PCT', ... % Pontine crossing tract (a part of MCP)
'3: GCC', ... % Genu of corpus callosum
'4: CCB', ... % Body of corpus callosum
'5: SCC', ... % Splenium of corpus callosum
'6: FX', ... % Fornix (column and body of fornix)
'7: CST_R', ... % Corticospinal tract R
'8: CST_L', ... % Corticospinal tract L
'9: ML_R', ... % Medial lemniscus R
'10: ML_L', ... % Medial lemniscus L
'11: ICP_R', ... % Inferior cerebellar peduncle R
'12: ICP_L', ... % Inferior cerebellar peduncle L
'13: SCP_R', ... % Superior cerebellar peduncle R
'14: SCP_L', ... % Superior cerebellar peduncle L
'15: CP_R', ... % Cerebral peduncle R
'16: CP_L', ... % Cerebral peduncle L
'17: ALIC_R', ... % Anterior limb of internal capsule R
'18: ALIC_L', ... % Anterior limb of internal capsule L
'19: PLIC_R', ... % Posterior limb of internal capsule R
'20: PLIC_L', ... % Posterior limb of internal capsule L
'21: RLIC_R', ... % Retrolenticular part of internal capsule R
'22: RLIC_L', ... % Retrolenticular part of internal capsule L
'23: ACR_R', ... % Anterior corona radiata R
'24: ACR_L', ... % Anterior corona radiata L
'25: SCR_R', ... % Superior corona radiata R
'26: SCR_L', ... % Superior corona radiata L
'27: PCR_R', ... % Posterior corona radiata R
'28: PCR_L', ... % Posterior corona radiata L
'29: PTR_R', ... % Posterior thalamic radiation (include optic radiation) R
'30: PTR_L', ... % Posterior thalamic radiation (include optic radiation) L
'31: SS_R', ... % Sagittal stratum (incl ILF and IFOF) R
'32: SS_L', ... % Sagittal stratum (incl ILF and IFOF) L
'33: EC_R', ... % External capsule R
'34: EC_L', ... % External capsule L
'35: CGC_R', ... % Cingulum (cingulate gyrus) R
'36: CGC_L', ... % Cingulum (cingulate gyrus) L
'37: CGH_R', ... % Cingulum (hippocampus) R
'38: CGH_L', ... % Cingulum (hippocampus) L
'39: FST_R', ... % Fornix (crus) / Stria terminalis R
'40: FST_L', ... % Fornix (crus) / Stria terminalis L
'41: SLF_R', ... % Superior longitudinal fasciculus R
'42: SLF_L', ... % Superior longitudinal fasciculus L
'43: SFOF_R', ... % Superior fronto-occipital fasciculus R
'44: SFOF_L', ... % Superior fronto-occipital fasciculus L
'45: UF_R', ... % Uncinate fasciculus R
'46: UF_L', ... % Uncinate fasciculus L
'47: TAP_R', ... % Tapetum R
'48: TAP_L' ... % Tapetum L
};




a = @(x) strsplit(x, ' ');
b = @(x,i) x{i};
c = @(x) str2num(x(1:(end-1)));

labels = cellfun(@(x) b(a(x),2), txt, 'UniformOutput', false);
ids = cellfun(@(x) c(b(a(x),1)), txt, 'UniformOutput', false);
end
end
end
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