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ARET/Allen_to_GroupSpace.m
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| function Allen_to_GroupSpace(Templates) | |
| % Description: Transformation of ANO file to group template space | |
| % -----------------------------------------% | |
| % Tanusree Chaudhuri | |
| % Max Planck Institute of Psychiatry, Munich | |
| % tanusree_chaudhuri@psych.mpg.de | |
| % -----------------------------------------% | |
| % ----------------------------------------------------------------------------------------% | |
| global DataDir; | |
| global TemplatesDir; | |
| % 1. Increase resolution of allen templates (TPMs,ANO) to match group template resolution% | |
| MC_change_voxel_size(Templates); | |
| % 2. Register TPMs to group template (Template_6) % | |
| matlabbatch{1}.spm.spatial.coreg.write.ref = cellstr(strcat(DataDir,'Template_6.nii,1')); | |
| matlabbatch{1}.spm.spatial.coreg.write.source = cellstr(Templates); | |
| matlabbatch{1}.spm.spatial.coreg.write.roptions.interp = 0; | |
| matlabbatch{1}.spm.spatial.coreg.write.roptions.wrap = [0 0 0]; | |
| matlabbatch{1}.spm.spatial.coreg.write.roptions.mask = 0; | |
| matlabbatch{1}.spm.spatial.coreg.write.roptions.prefix = 'r'; | |
| spm_jobman('run',matlabbatch); | |
| % Generate deformation fields (u_* files) % | |
| Registered_Templates = {strcat(TemplatesDir,'r_b1grey.nii,1');strcat(TemplatesDir,'r_b2white.nii,1')}; | |
| matlabbatch{1}.spm.tools.dartel.warp1.images = cellstr(Registered_Templates); | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.rform = 0; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(1).its = 3; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(1).rparam = [4 2 1e-06]; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(1).K = 0; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(1).template = cellstr(strcat(DataDir,'Template_0.nii')); | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(2).its = 3; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(2).rparam = [2 1 1e-06]; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(2).K = 0; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(2).template = cellstr(strcat(DataDir,'Template_1.nii')); | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(3).its = 3; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(3).rparam = [1 0.5 1e-06]; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(3).K = 1; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(3).template = cellstr(strcat(DataDir,'Template_2.nii')); | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(4).its = 3; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(4).rparam = [0.5 0.25 1e-06]; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(4).K = 2; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(4).template = cellstr(strcat(DataDir,'Template_3.nii')); | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(5).its = 3; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(5).rparam = [0.25 0.125 1e-06]; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(5).K = 4; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(5).template = cellstr(strcat(DataDir,'Template_4.nii')); | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(6).its = 3; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(6).rparam = [0.25 0.125 1e-06]; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(6).K = 6; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.param(6).template = cellstr(strcat(DataDir,'Template_6.nii')); | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.optim.lmreg = 0.01; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.optim.cyc = 3; | |
| matlabbatch{1}.spm.tools.dartel.warp1.settings.optim.its = 3; | |
| spm_jobman('run',matlabbatch); | |
| % 3. Normalise registered TPMs & ANO to group template space % | |
| matlabbatch{1}.spm.tools.dartel.crt_warped.flowfields = cellstr(strcat(TemplatesDir,'u_r_b1grey.nii')); | |
| TemplatesToWarp = {strcat(TemplatesDir,'r_b1grey.nii,1'); strcat(TemplatesDir,'r_b2white.nii,1');strcat(TemplatesDir,'ANO.nii')}; | |
| matlabbatch{1}.spm.tools.dartel.crt_warped.images = cellstr(TemplatesToWarp); | |
| matlabbatch{1}.spm.tools.dartel.crt_warped.jactransf = 0; | |
| matlabbatch{1}.spm.tools.dartel.crt_warped.K = 6; | |
| matlabbatch{1}.spm.tools.dartel.crt_warped.interp = 0; | |
| spm_jobman('run',matlabbatch); |