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mantis_complete_segmentation8.m
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%-----------------------------------------------------------------------
% Job configuration created by cfg_util (rev $Rev: 4252 $)
%-----------------------------------------------------------------------
matlabbatch{1}.cfg_basicio.cfg_named_file.name = 'Structural scans';
matlabbatch{1}.cfg_basicio.cfg_named_file.files = {{}};
matlabbatch{2}.spm.tools.mantis.phasefolders.vols(1) = cfg_dep;
matlabbatch{2}.spm.tools.mantis.phasefolders.vols(1).tname = 'Volumes';
matlabbatch{2}.spm.tools.mantis.phasefolders.vols(1).tgt_spec{1}(1).name = 'class';
matlabbatch{2}.spm.tools.mantis.phasefolders.vols(1).tgt_spec{1}(1).value = 'cfg_files';
matlabbatch{2}.spm.tools.mantis.phasefolders.vols(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{2}.spm.tools.mantis.phasefolders.vols(1).tgt_spec{1}(2).value = 'e';
matlabbatch{2}.spm.tools.mantis.phasefolders.vols(1).sname = 'Named File Selector: Structural scans(1) - Files';
matlabbatch{2}.spm.tools.mantis.phasefolders.vols(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{2}.spm.tools.mantis.phasefolders.vols(1).src_output = substruct('.','files', '{}',{1});
matlabbatch{3}.spm.tools.mantis.neonatetemplate = struct([]);
matlabbatch{4}.spm.tools.mantis.phase1.channel.vols(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.channel.vols(1).tname = 'Volumes';
matlabbatch{4}.spm.tools.mantis.phase1.channel.vols(1).tgt_spec{1}(1).name = 'class';
matlabbatch{4}.spm.tools.mantis.phase1.channel.vols(1).tgt_spec{1}(1).value = 'cfg_files';
matlabbatch{4}.spm.tools.mantis.phase1.channel.vols(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.channel.vols(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.channel.vols(1).sname = 'Named File Selector: Structural scans(1) - Files';
matlabbatch{4}.spm.tools.mantis.phase1.channel.vols(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.channel.vols(1).src_output = substruct('.','files', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.channel.biasreg = 0.0001;
matlabbatch{4}.spm.tools.mantis.phase1.channel.biasfwhm = 60;
matlabbatch{4}.spm.tools.mantis.phase1.channel.write = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).tpm(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).tpm(1).tname = 'Tissue probability map';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).tpm(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).tpm(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).tpm(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).tpm(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).tpm(1).sname = 'Path for all components of the neonate template: Neonate template channel 1';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).tpm(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).tpm(1).src_output = substruct('.','tissuemap', '()',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).ngaus = 2;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).native = [1 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(1).warped = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).tpm(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).tpm(1).tname = 'Tissue probability map';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).tpm(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).tpm(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).tpm(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).tpm(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).tpm(1).sname = 'Path for all components of the neonate template: Neonate template channel 2';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).tpm(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).tpm(1).src_output = substruct('.','tissuemap', '()',{2});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).ngaus = 2;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).native = [1 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(2).warped = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).tpm(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).tpm(1).tname = 'Tissue probability map';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).tpm(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).tpm(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).tpm(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).tpm(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).tpm(1).sname = 'Path for all components of the neonate template: Neonate template channel 3';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).tpm(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).tpm(1).src_output = substruct('.','tissuemap', '()',{3});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).ngaus = 2;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).native = [1 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(3).warped = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).tpm(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).tpm(1).tname = 'Tissue probability map';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).tpm(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).tpm(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).tpm(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).tpm(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).tpm(1).sname = 'Path for all components of the neonate template: Neonate template channel 4';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).tpm(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).tpm(1).src_output = substruct('.','tissuemap', '()',{4});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).ngaus = 2;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).native = [1 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(4).warped = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).tpm(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).tpm(1).tname = 'Tissue probability map';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).tpm(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).tpm(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).tpm(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).tpm(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).tpm(1).sname = 'Path for all components of the neonate template: Neonate template channel 5';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).tpm(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).tpm(1).src_output = substruct('.','tissuemap', '()',{5});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).ngaus = 2;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).native = [1 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(5).warped = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).tpm(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).tpm(1).tname = 'Tissue probability map';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).tpm(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).tpm(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).tpm(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).tpm(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).tpm(1).sname = 'Path for all components of the neonate template: Neonate template channel 6';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).tpm(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).tpm(1).src_output = substruct('.','tissuemap', '()',{6});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).ngaus = 2;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).native = [1 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(6).warped = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).tpm(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).tpm(1).tname = 'Tissue probability map';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).tpm(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).tpm(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).tpm(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).tpm(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).tpm(1).sname = 'Path for all components of the neonate template: Neonate template channel 7';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).tpm(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).tpm(1).src_output = substruct('.','tissuemap', '()',{7});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).ngaus = 2;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).native = [1 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(7).warped = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).tpm(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).tpm(1).tname = 'Tissue probability map';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).tpm(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).tpm(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).tpm(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).tpm(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).tpm(1).sname = 'Path for all components of the neonate template: Neonate template channel 8';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).tpm(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).tpm(1).src_output = substruct('.','tissuemap', '()',{8});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).ngaus = 2;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).native = [1 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(8).warped = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).tpm(1) = cfg_dep;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).tpm(1).tname = 'Tissue probability map';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).tpm(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).tpm(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).tpm(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).tpm(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).tpm(1).sname = 'Path for all components of the neonate template: Neonate template channel 9';
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).tpm(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).tpm(1).src_output = substruct('.','tissuemap', '()',{9});
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).ngaus = 2;
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).native = [1 0];
matlabbatch{4}.spm.tools.mantis.phase1.tissue(9).warped = [0 0];
matlabbatch{4}.spm.tools.mantis.phase1.warp.mrf = 0;
matlabbatch{4}.spm.tools.mantis.phase1.warp.reg = 4;
matlabbatch{4}.spm.tools.mantis.phase1.warp.affreg = 'mni';
matlabbatch{4}.spm.tools.mantis.phase1.warp.samp = 3;
matlabbatch{4}.spm.tools.mantis.phase1.warp.write = [1 1];
matlabbatch{5}.cfg_basicio.file_move.files(1) = cfg_dep;
matlabbatch{5}.cfg_basicio.file_move.files(1).tname = 'Files to move/copy/delete';
matlabbatch{5}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{5}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).value = 'mat';
matlabbatch{5}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{5}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).value = 'e';
matlabbatch{5}.cfg_basicio.file_move.files(1).sname = 'Mantis: Phase 1 tissue classification: Seg Params';
matlabbatch{5}.cfg_basicio.file_move.files(1).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{5}.cfg_basicio.file_move.files(1).src_output = substruct('.','param', '()',{':'});
matlabbatch{5}.cfg_basicio.file_move.action.moveto(1) = cfg_dep;
matlabbatch{5}.cfg_basicio.file_move.action.moveto(1).tname = 'Move to';
matlabbatch{5}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{5}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{5}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{5}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).value = 'e';
matlabbatch{5}.cfg_basicio.file_move.action.moveto(1).sname = 'Folders for phases - image files get placed here: Phase1 single subfolder';
matlabbatch{5}.cfg_basicio.file_move.action.moveto(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{5}.cfg_basicio.file_move.action.moveto(1).src_output = substruct('.','outpathphase1', '()',{1});
matlabbatch{6}.cfg_basicio.file_move.files(1) = cfg_dep;
matlabbatch{6}.cfg_basicio.file_move.files(1).tname = 'Files to move/copy/delete';
matlabbatch{6}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{6}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).value = 'image';
matlabbatch{6}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{6}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).value = 'e';
matlabbatch{6}.cfg_basicio.file_move.files(1).sname = 'Mantis: Phase 1 tissue classification: c1 Images';
matlabbatch{6}.cfg_basicio.file_move.files(1).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{6}.cfg_basicio.file_move.files(1).src_output = substruct('.','tiss', '()',{1}, '.','c', '()',{':'});
matlabbatch{6}.cfg_basicio.file_move.action.moveto(1) = cfg_dep;
matlabbatch{6}.cfg_basicio.file_move.action.moveto(1).tname = 'Move to';
matlabbatch{6}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{6}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{6}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{6}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).value = 'e';
matlabbatch{6}.cfg_basicio.file_move.action.moveto(1).sname = 'Folders for phases - image files get placed here: Phase1 single subfolder';
matlabbatch{6}.cfg_basicio.file_move.action.moveto(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{6}.cfg_basicio.file_move.action.moveto(1).src_output = substruct('.','outpathphase1', '()',{1});
matlabbatch{7}.cfg_basicio.file_move.files(1) = cfg_dep;
matlabbatch{7}.cfg_basicio.file_move.files(1).tname = 'Files to move/copy/delete';
matlabbatch{7}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{7}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).value = 'image';
matlabbatch{7}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{7}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).value = 'e';
matlabbatch{7}.cfg_basicio.file_move.files(1).sname = 'Mantis: Phase 1 tissue classification: c3 Images';
matlabbatch{7}.cfg_basicio.file_move.files(1).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{7}.cfg_basicio.file_move.files(1).src_output = substruct('.','tiss', '()',{3}, '.','c', '()',{':'});
matlabbatch{7}.cfg_basicio.file_move.action.moveto(1) = cfg_dep;
matlabbatch{7}.cfg_basicio.file_move.action.moveto(1).tname = 'Move to';
matlabbatch{7}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{7}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{7}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{7}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).value = 'e';
matlabbatch{7}.cfg_basicio.file_move.action.moveto(1).sname = 'Folders for phases - image files get placed here: Phase1 single subfolder';
matlabbatch{7}.cfg_basicio.file_move.action.moveto(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{7}.cfg_basicio.file_move.action.moveto(1).src_output = substruct('.','outpathphase1', '()',{1});
matlabbatch{8}.cfg_basicio.file_move.files(1) = cfg_dep;
matlabbatch{8}.cfg_basicio.file_move.files(1).tname = 'Files to move/copy/delete';
matlabbatch{8}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{8}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).value = 'image';
matlabbatch{8}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{8}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).value = 'e';
matlabbatch{8}.cfg_basicio.file_move.files(1).sname = 'Mantis: Phase 1 tissue classification: c2 Images';
matlabbatch{8}.cfg_basicio.file_move.files(1).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{8}.cfg_basicio.file_move.files(1).src_output = substruct('.','tiss', '()',{2}, '.','c', '()',{':'});
matlabbatch{8}.cfg_basicio.file_move.files(2) = cfg_dep;
matlabbatch{8}.cfg_basicio.file_move.files(2).tname = 'Files to move/copy/delete';
matlabbatch{8}.cfg_basicio.file_move.files(2).tgt_spec{1}(1).name = 'filter';
matlabbatch{8}.cfg_basicio.file_move.files(2).tgt_spec{1}(1).value = 'image';
matlabbatch{8}.cfg_basicio.file_move.files(2).tgt_spec{1}(2).name = 'strtype';
matlabbatch{8}.cfg_basicio.file_move.files(2).tgt_spec{1}(2).value = 'e';
matlabbatch{8}.cfg_basicio.file_move.files(2).sname = 'Mantis: Phase 1 tissue classification: c4 Images';
matlabbatch{8}.cfg_basicio.file_move.files(2).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{8}.cfg_basicio.file_move.files(2).src_output = substruct('.','tiss', '()',{4}, '.','c', '()',{':'});
matlabbatch{8}.cfg_basicio.file_move.files(3) = cfg_dep;
matlabbatch{8}.cfg_basicio.file_move.files(3).tname = 'Files to move/copy/delete';
matlabbatch{8}.cfg_basicio.file_move.files(3).tgt_spec{1}(1).name = 'filter';
matlabbatch{8}.cfg_basicio.file_move.files(3).tgt_spec{1}(1).value = 'image';
matlabbatch{8}.cfg_basicio.file_move.files(3).tgt_spec{1}(2).name = 'strtype';
matlabbatch{8}.cfg_basicio.file_move.files(3).tgt_spec{1}(2).value = 'e';
matlabbatch{8}.cfg_basicio.file_move.files(3).sname = 'Mantis: Phase 1 tissue classification: c5 Images';
matlabbatch{8}.cfg_basicio.file_move.files(3).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{8}.cfg_basicio.file_move.files(3).src_output = substruct('.','tiss', '()',{5}, '.','c', '()',{':'});
matlabbatch{8}.cfg_basicio.file_move.files(4) = cfg_dep;
matlabbatch{8}.cfg_basicio.file_move.files(4).tname = 'Files to move/copy/delete';
matlabbatch{8}.cfg_basicio.file_move.files(4).tgt_spec{1}(1).name = 'filter';
matlabbatch{8}.cfg_basicio.file_move.files(4).tgt_spec{1}(1).value = 'image';
matlabbatch{8}.cfg_basicio.file_move.files(4).tgt_spec{1}(2).name = 'strtype';
matlabbatch{8}.cfg_basicio.file_move.files(4).tgt_spec{1}(2).value = 'e';
matlabbatch{8}.cfg_basicio.file_move.files(4).sname = 'Mantis: Phase 1 tissue classification: c6 Images';
matlabbatch{8}.cfg_basicio.file_move.files(4).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{8}.cfg_basicio.file_move.files(4).src_output = substruct('.','tiss', '()',{6}, '.','c', '()',{':'});
matlabbatch{8}.cfg_basicio.file_move.files(5) = cfg_dep;
matlabbatch{8}.cfg_basicio.file_move.files(5).tname = 'Files to move/copy/delete';
matlabbatch{8}.cfg_basicio.file_move.files(5).tgt_spec{1}(1).name = 'filter';
matlabbatch{8}.cfg_basicio.file_move.files(5).tgt_spec{1}(1).value = 'image';
matlabbatch{8}.cfg_basicio.file_move.files(5).tgt_spec{1}(2).name = 'strtype';
matlabbatch{8}.cfg_basicio.file_move.files(5).tgt_spec{1}(2).value = 'e';
matlabbatch{8}.cfg_basicio.file_move.files(5).sname = 'Mantis: Phase 1 tissue classification: c7 Images';
matlabbatch{8}.cfg_basicio.file_move.files(5).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{8}.cfg_basicio.file_move.files(5).src_output = substruct('.','tiss', '()',{7}, '.','c', '()',{':'});
matlabbatch{8}.cfg_basicio.file_move.files(6) = cfg_dep;
matlabbatch{8}.cfg_basicio.file_move.files(6).tname = 'Files to move/copy/delete';
matlabbatch{8}.cfg_basicio.file_move.files(6).tgt_spec{1}(1).name = 'filter';
matlabbatch{8}.cfg_basicio.file_move.files(6).tgt_spec{1}(1).value = 'image';
matlabbatch{8}.cfg_basicio.file_move.files(6).tgt_spec{1}(2).name = 'strtype';
matlabbatch{8}.cfg_basicio.file_move.files(6).tgt_spec{1}(2).value = 'e';
matlabbatch{8}.cfg_basicio.file_move.files(6).sname = 'Mantis: Phase 1 tissue classification: c8 Images';
matlabbatch{8}.cfg_basicio.file_move.files(6).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{8}.cfg_basicio.file_move.files(6).src_output = substruct('.','tiss', '()',{8}, '.','c', '()',{':'});
matlabbatch{8}.cfg_basicio.file_move.files(7) = cfg_dep;
matlabbatch{8}.cfg_basicio.file_move.files(7).tname = 'Files to move/copy/delete';
matlabbatch{8}.cfg_basicio.file_move.files(7).tgt_spec{1}(1).name = 'filter';
matlabbatch{8}.cfg_basicio.file_move.files(7).tgt_spec{1}(1).value = 'image';
matlabbatch{8}.cfg_basicio.file_move.files(7).tgt_spec{1}(2).name = 'strtype';
matlabbatch{8}.cfg_basicio.file_move.files(7).tgt_spec{1}(2).value = 'e';
matlabbatch{8}.cfg_basicio.file_move.files(7).sname = 'Mantis: Phase 1 tissue classification: c9 Images';
matlabbatch{8}.cfg_basicio.file_move.files(7).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{8}.cfg_basicio.file_move.files(7).src_output = substruct('.','tiss', '()',{9}, '.','c', '()',{':'});
matlabbatch{8}.cfg_basicio.file_move.action.moveto(1) = cfg_dep;
matlabbatch{8}.cfg_basicio.file_move.action.moveto(1).tname = 'Move to';
matlabbatch{8}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{8}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{8}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{8}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).value = 'e';
matlabbatch{8}.cfg_basicio.file_move.action.moveto(1).sname = 'Folders for phases - image files get placed here: Phase1 single subfolder';
matlabbatch{8}.cfg_basicio.file_move.action.moveto(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{8}.cfg_basicio.file_move.action.moveto(1).src_output = substruct('.','outpathphase1', '()',{1});
matlabbatch{9}.cfg_basicio.file_move.files(1) = cfg_dep;
matlabbatch{9}.cfg_basicio.file_move.files(1).tname = 'Files to move/copy/delete';
matlabbatch{9}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{9}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).value = 'image';
matlabbatch{9}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{9}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).value = 'e';
matlabbatch{9}.cfg_basicio.file_move.files(1).sname = 'Mantis: Phase 1 tissue classification: Forward Deformations';
matlabbatch{9}.cfg_basicio.file_move.files(1).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{9}.cfg_basicio.file_move.files(1).src_output = substruct('.','fordef', '()',{':'});
matlabbatch{9}.cfg_basicio.file_move.action.moveto(1) = cfg_dep;
matlabbatch{9}.cfg_basicio.file_move.action.moveto(1).tname = 'Move to';
matlabbatch{9}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{9}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{9}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{9}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).value = 'e';
matlabbatch{9}.cfg_basicio.file_move.action.moveto(1).sname = 'Folders for phases - image files get placed here: Phase1 single subfolder';
matlabbatch{9}.cfg_basicio.file_move.action.moveto(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{9}.cfg_basicio.file_move.action.moveto(1).src_output = substruct('.','outpathphase1', '()',{1});
matlabbatch{10}.cfg_basicio.file_move.files(1) = cfg_dep;
matlabbatch{10}.cfg_basicio.file_move.files(1).tname = 'Files to move/copy/delete';
matlabbatch{10}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{10}.cfg_basicio.file_move.files(1).tgt_spec{1}(1).value = 'image';
matlabbatch{10}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{10}.cfg_basicio.file_move.files(1).tgt_spec{1}(2).value = 'e';
matlabbatch{10}.cfg_basicio.file_move.files(1).sname = 'Mantis: Phase 1 tissue classification: Inverse Deformations';
matlabbatch{10}.cfg_basicio.file_move.files(1).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{10}.cfg_basicio.file_move.files(1).src_output = substruct('.','invdef', '()',{':'});
matlabbatch{10}.cfg_basicio.file_move.action.moveto(1) = cfg_dep;
matlabbatch{10}.cfg_basicio.file_move.action.moveto(1).tname = 'Move to';
matlabbatch{10}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{10}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{10}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{10}.cfg_basicio.file_move.action.moveto(1).tgt_spec{1}(2).value = 'e';
matlabbatch{10}.cfg_basicio.file_move.action.moveto(1).sname = 'Folders for phases - image files get placed here: Phase1 single subfolder';
matlabbatch{10}.cfg_basicio.file_move.action.moveto(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{10}.cfg_basicio.file_move.action.moveto(1).src_output = substruct('.','outpathphase1', '()',{1});
matlabbatch{11}.spm.tools.mantis.wscsf.vols(1) = cfg_dep;
matlabbatch{11}.spm.tools.mantis.wscsf.vols(1).tname = 'Volumes';
matlabbatch{11}.spm.tools.mantis.wscsf.vols(1).tgt_spec{1}(1).name = 'class';
matlabbatch{11}.spm.tools.mantis.wscsf.vols(1).tgt_spec{1}(1).value = 'cfg_files';
matlabbatch{11}.spm.tools.mantis.wscsf.vols(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{11}.spm.tools.mantis.wscsf.vols(1).tgt_spec{1}(2).value = 'e';
matlabbatch{11}.spm.tools.mantis.wscsf.vols(1).sname = 'Named File Selector: Structural scans(1) - Files';
matlabbatch{11}.spm.tools.mantis.wscsf.vols(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{11}.spm.tools.mantis.wscsf.vols(1).src_output = substruct('.','files', '{}',{1});
matlabbatch{11}.spm.tools.mantis.wscsf.parent(1) = cfg_dep;
matlabbatch{11}.spm.tools.mantis.wscsf.parent(1).tname = 'Parent Directory';
matlabbatch{11}.spm.tools.mantis.wscsf.parent(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{11}.spm.tools.mantis.wscsf.parent(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{11}.spm.tools.mantis.wscsf.parent(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{11}.spm.tools.mantis.wscsf.parent(1).tgt_spec{1}(2).value = 'e';
matlabbatch{11}.spm.tools.mantis.wscsf.parent(1).sname = 'Folders for phases - image files get placed here: Phase1 subfolder';
matlabbatch{11}.spm.tools.mantis.wscsf.parent(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{11}.spm.tools.mantis.wscsf.parent(1).src_output = substruct('.','outpathphase1', '()',{':'});
matlabbatch{11}.spm.tools.mantis.wscsf.target(1) = cfg_dep;
matlabbatch{11}.spm.tools.mantis.wscsf.target(1).tname = 'Target Directory';
matlabbatch{11}.spm.tools.mantis.wscsf.target(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{11}.spm.tools.mantis.wscsf.target(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{11}.spm.tools.mantis.wscsf.target(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{11}.spm.tools.mantis.wscsf.target(1).tgt_spec{1}(2).value = 'e';
matlabbatch{11}.spm.tools.mantis.wscsf.target(1).sname = 'Folders for phases - image files get placed here: Phase2 subfolder';
matlabbatch{11}.spm.tools.mantis.wscsf.target(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{11}.spm.tools.mantis.wscsf.target(1).src_output = substruct('.','outpathphase2', '()',{':'});
matlabbatch{12}.spm.tools.mantis.wmclean.vols(1) = cfg_dep;
matlabbatch{12}.spm.tools.mantis.wmclean.vols(1).tname = 'Volumes';
matlabbatch{12}.spm.tools.mantis.wmclean.vols(1).tgt_spec{1}(1).name = 'class';
matlabbatch{12}.spm.tools.mantis.wmclean.vols(1).tgt_spec{1}(1).value = 'cfg_files';
matlabbatch{12}.spm.tools.mantis.wmclean.vols(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{12}.spm.tools.mantis.wmclean.vols(1).tgt_spec{1}(2).value = 'e';
matlabbatch{12}.spm.tools.mantis.wmclean.vols(1).sname = 'Named File Selector: Structural scans(1) - Files';
matlabbatch{12}.spm.tools.mantis.wmclean.vols(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{12}.spm.tools.mantis.wmclean.vols(1).src_output = substruct('.','files', '{}',{1});
matlabbatch{12}.spm.tools.mantis.wmclean.parent(1) = cfg_dep;
matlabbatch{12}.spm.tools.mantis.wmclean.parent(1).tname = 'Parent Directory';
matlabbatch{12}.spm.tools.mantis.wmclean.parent(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{12}.spm.tools.mantis.wmclean.parent(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{12}.spm.tools.mantis.wmclean.parent(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{12}.spm.tools.mantis.wmclean.parent(1).tgt_spec{1}(2).value = 'e';
matlabbatch{12}.spm.tools.mantis.wmclean.parent(1).sname = 'Folders for phases - image files get placed here: Phase1 subfolder';
matlabbatch{12}.spm.tools.mantis.wmclean.parent(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{12}.spm.tools.mantis.wmclean.parent(1).src_output = substruct('.','outpathphase1', '()',{':'});
matlabbatch{12}.spm.tools.mantis.wmclean.target(1) = cfg_dep;
matlabbatch{12}.spm.tools.mantis.wmclean.target(1).tname = 'Target Directory';
matlabbatch{12}.spm.tools.mantis.wmclean.target(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{12}.spm.tools.mantis.wmclean.target(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{12}.spm.tools.mantis.wmclean.target(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{12}.spm.tools.mantis.wmclean.target(1).tgt_spec{1}(2).value = 'e';
matlabbatch{12}.spm.tools.mantis.wmclean.target(1).sname = 'Folders for phases - image files get placed here: Phase2 subfolder';
matlabbatch{12}.spm.tools.mantis.wmclean.target(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{12}.spm.tools.mantis.wmclean.target(1).src_output = substruct('.','outpathphase2', '()',{':'});
matlabbatch{13}.spm.tools.mantis.neonatefirstnorm = struct([]);
matlabbatch{14}.spm.tools.mantis.defs.def(1) = cfg_dep;
matlabbatch{14}.spm.tools.mantis.defs.def(1).tname = 'Deformation Field';
matlabbatch{14}.spm.tools.mantis.defs.def(1).tgt_spec{1}(1).name = 'class';
matlabbatch{14}.spm.tools.mantis.defs.def(1).tgt_spec{1}(1).value = 'cfg_files';
matlabbatch{14}.spm.tools.mantis.defs.def(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{14}.spm.tools.mantis.defs.def(1).tgt_spec{1}(2).value = 'e';
matlabbatch{14}.spm.tools.mantis.defs.def(1).sname = 'Move/Delete Files: Moved/Copied Files';
matlabbatch{14}.spm.tools.mantis.defs.def(1).src_exbranch = substruct('.','val', '{}',{10}, '.','val', '{}',{1});
matlabbatch{14}.spm.tools.mantis.defs.def(1).src_output = substruct('.','files');
matlabbatch{14}.spm.tools.mantis.defs.fnames(1) = cfg_dep;
matlabbatch{14}.spm.tools.mantis.defs.fnames(1).tname = 'Apply to';
matlabbatch{14}.spm.tools.mantis.defs.fnames(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{14}.spm.tools.mantis.defs.fnames(1).tgt_spec{1}(1).value = 'image';
matlabbatch{14}.spm.tools.mantis.defs.fnames(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{14}.spm.tools.mantis.defs.fnames(1).tgt_spec{1}(2).value = 'e';
matlabbatch{14}.spm.tools.mantis.defs.fnames(1).sname = 'Path for all components of the neonate firstnorm: Neonate firstnorm';
matlabbatch{14}.spm.tools.mantis.defs.fnames(1).src_exbranch = substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{14}.spm.tools.mantis.defs.fnames(1).src_output = substruct('.','tissuemap', '()',{':'});
matlabbatch{14}.spm.tools.mantis.defs.saveusr(1) = cfg_dep;
matlabbatch{14}.spm.tools.mantis.defs.saveusr(1).tname = 'Output directory';
matlabbatch{14}.spm.tools.mantis.defs.saveusr(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{14}.spm.tools.mantis.defs.saveusr(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{14}.spm.tools.mantis.defs.saveusr(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{14}.spm.tools.mantis.defs.saveusr(1).tgt_spec{1}(2).value = 'e';
matlabbatch{14}.spm.tools.mantis.defs.saveusr(1).sname = 'Folders for phases - image files get placed here: Phase2 single subfolder';
matlabbatch{14}.spm.tools.mantis.defs.saveusr(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{14}.spm.tools.mantis.defs.saveusr(1).src_output = substruct('.','outpathphase2', '()',{1});
matlabbatch{14}.spm.tools.mantis.defs.interp = 1;
matlabbatch{15}.spm.tools.mantis.maketpm.vols(1) = cfg_dep;
matlabbatch{15}.spm.tools.mantis.maketpm.vols(1).tname = 'Volumes';
matlabbatch{15}.spm.tools.mantis.maketpm.vols(1).tgt_spec{1}(1).name = 'class';
matlabbatch{15}.spm.tools.mantis.maketpm.vols(1).tgt_spec{1}(1).value = 'cfg_files';
matlabbatch{15}.spm.tools.mantis.maketpm.vols(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{15}.spm.tools.mantis.maketpm.vols(1).tgt_spec{1}(2).value = 'e';
matlabbatch{15}.spm.tools.mantis.maketpm.vols(1).sname = 'Named File Selector: Structural scans(1) - Files';
matlabbatch{15}.spm.tools.mantis.maketpm.vols(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{15}.spm.tools.mantis.maketpm.vols(1).src_output = substruct('.','files', '{}',{1});
matlabbatch{15}.spm.tools.mantis.maketpm.parent(1) = cfg_dep;
matlabbatch{15}.spm.tools.mantis.maketpm.parent(1).tname = 'Parent Directory';
matlabbatch{15}.spm.tools.mantis.maketpm.parent(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{15}.spm.tools.mantis.maketpm.parent(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{15}.spm.tools.mantis.maketpm.parent(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{15}.spm.tools.mantis.maketpm.parent(1).tgt_spec{1}(2).value = 'e';
matlabbatch{15}.spm.tools.mantis.maketpm.parent(1).sname = 'Folders for phases - image files get placed here: Phase1 subfolder';
matlabbatch{15}.spm.tools.mantis.maketpm.parent(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{15}.spm.tools.mantis.maketpm.parent(1).src_output = substruct('.','outpathphase1', '()',{':'});
matlabbatch{15}.spm.tools.mantis.maketpm.target(1) = cfg_dep;
matlabbatch{15}.spm.tools.mantis.maketpm.target(1).tname = 'Target Directory';
matlabbatch{15}.spm.tools.mantis.maketpm.target(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{15}.spm.tools.mantis.maketpm.target(1).tgt_spec{1}(1).value = 'dir';
matlabbatch{15}.spm.tools.mantis.maketpm.target(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{15}.spm.tools.mantis.maketpm.target(1).tgt_spec{1}(2).value = 'e';
matlabbatch{15}.spm.tools.mantis.maketpm.target(1).sname = 'Folders for phases - image files get placed here: Phase2 subfolder';
matlabbatch{15}.spm.tools.mantis.maketpm.target(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{15}.spm.tools.mantis.maketpm.target(1).src_output = substruct('.','outpathphase2', '()',{':'});
matlabbatch{16}.spm.tools.mantis.tissueclassif2.vols(1) = cfg_dep;
matlabbatch{16}.spm.tools.mantis.tissueclassif2.vols(1).tname = 'Volumes';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.vols(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.vols(1).tgt_spec{1}(1).value = 'image';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.vols(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.vols(1).tgt_spec{1}(2).value = 'e';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.vols(1).sname = 'Morphogical clean up of White matter: Clean up of white matter';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.vols(1).src_exbranch = substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{16}.spm.tools.mantis.tissueclassif2.vols(1).src_output = substruct('.','wmclean', '()',{':'});
matlabbatch{16}.spm.tools.mantis.tissueclassif2.tmaps(1) = cfg_dep;
matlabbatch{16}.spm.tools.mantis.tissueclassif2.tmaps(1).tname = 'Tissue maps';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.tmaps(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.tmaps(1).tgt_spec{1}(1).value = 'image';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.tmaps(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.tmaps(1).tgt_spec{1}(2).value = 'e';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.tmaps(1).sname = 'Make subject specific template: Subject template';
matlabbatch{16}.spm.tools.mantis.tissueclassif2.tmaps(1).src_exbranch = substruct('.','val', '{}',{15}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{16}.spm.tools.mantis.tissueclassif2.tmaps(1).src_output = substruct('.','tissuemap', '()',{':'});
matlabbatch{17}.spm.tools.mantis.hardseg1.vols(1) = cfg_dep;
matlabbatch{17}.spm.tools.mantis.hardseg1.vols(1).tname = 'Tissue maps';
matlabbatch{17}.spm.tools.mantis.hardseg1.vols(1).tgt_spec{1}(1).name = 'class';
matlabbatch{17}.spm.tools.mantis.hardseg1.vols(1).tgt_spec{1}(1).value = 'cfg_files';
matlabbatch{17}.spm.tools.mantis.hardseg1.vols(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{17}.spm.tools.mantis.hardseg1.vols(1).tgt_spec{1}(2).value = 'e';
matlabbatch{17}.spm.tools.mantis.hardseg1.vols(1).sname = 'Move/Delete Files: Moved/Copied Files';
matlabbatch{17}.spm.tools.mantis.hardseg1.vols(1).src_exbranch = substruct('.','val', '{}',{6}, '.','val', '{}',{1});
matlabbatch{17}.spm.tools.mantis.hardseg1.vols(1).src_output = substruct('.','files');
matlabbatch{17}.spm.tools.mantis.hardseg1.structural(1) = cfg_dep;
matlabbatch{17}.spm.tools.mantis.hardseg1.structural(1).tname = 'Structural volumes';
matlabbatch{17}.spm.tools.mantis.hardseg1.structural(1).tgt_spec{1}(1).name = 'class';
matlabbatch{17}.spm.tools.mantis.hardseg1.structural(1).tgt_spec{1}(1).value = 'cfg_files';
matlabbatch{17}.spm.tools.mantis.hardseg1.structural(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{17}.spm.tools.mantis.hardseg1.structural(1).tgt_spec{1}(2).value = 'e';
matlabbatch{17}.spm.tools.mantis.hardseg1.structural(1).sname = 'Named File Selector: Structural scans(1) - Files';
matlabbatch{17}.spm.tools.mantis.hardseg1.structural(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{17}.spm.tools.mantis.hardseg1.structural(1).src_output = substruct('.','files', '{}',{1});
matlabbatch{18}.spm.tools.mantis.hardseg2.vols(1) = cfg_dep;
matlabbatch{18}.spm.tools.mantis.hardseg2.vols(1).tname = 'Tissue maps';
matlabbatch{18}.spm.tools.mantis.hardseg2.vols(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{18}.spm.tools.mantis.hardseg2.vols(1).tgt_spec{1}(1).value = 'image';
matlabbatch{18}.spm.tools.mantis.hardseg2.vols(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{18}.spm.tools.mantis.hardseg2.vols(1).tgt_spec{1}(2).value = 'e';
matlabbatch{18}.spm.tools.mantis.hardseg2.vols(1).sname = 'Final spm segmentation: Classification with patient specific template c1';
matlabbatch{18}.spm.tools.mantis.hardseg2.vols(1).src_exbranch = substruct('.','val', '{}',{16}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{18}.spm.tools.mantis.hardseg2.vols(1).src_output = substruct('.','patientspecifictemplateseg', '{}',{1});
matlabbatch{18}.spm.tools.mantis.hardseg2.structural(1) = cfg_dep;
matlabbatch{18}.spm.tools.mantis.hardseg2.structural(1).tname = 'Structural volumes';
matlabbatch{18}.spm.tools.mantis.hardseg2.structural(1).tgt_spec{1}(1).name = 'class';
matlabbatch{18}.spm.tools.mantis.hardseg2.structural(1).tgt_spec{1}(1).value = 'cfg_files';
matlabbatch{18}.spm.tools.mantis.hardseg2.structural(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{18}.spm.tools.mantis.hardseg2.structural(1).tgt_spec{1}(2).value = 'e';
matlabbatch{18}.spm.tools.mantis.hardseg2.structural(1).sname = 'Named File Selector: Structural scans(1) - Files';
matlabbatch{18}.spm.tools.mantis.hardseg2.structural(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{18}.spm.tools.mantis.hardseg2.structural(1).src_output = substruct('.','files', '{}',{1});
matlabbatch{18}.spm.tools.mantis.hardseg2.hardseg1(1) = cfg_dep;
matlabbatch{18}.spm.tools.mantis.hardseg2.hardseg1(1).tname = 'Phase 1 hard segmentation';
matlabbatch{18}.spm.tools.mantis.hardseg2.hardseg1(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{18}.spm.tools.mantis.hardseg2.hardseg1(1).tgt_spec{1}(1).value = 'image';
matlabbatch{18}.spm.tools.mantis.hardseg2.hardseg1(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{18}.spm.tools.mantis.hardseg2.hardseg1(1).tgt_spec{1}(2).value = 'e';
matlabbatch{18}.spm.tools.mantis.hardseg2.hardseg1(1).sname = 'Hard segmentation of phase 1: Hard seg phase 1 - GM';
matlabbatch{18}.spm.tools.mantis.hardseg2.hardseg1(1).src_exbranch = substruct('.','val', '{}',{17}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{18}.spm.tools.mantis.hardseg2.hardseg1(1).src_output = substruct('.','hard1', '()',{':'});