dartel_pipeline.m

%% ---------- Atlas Normalisation from Native to Allen space using DARTEL------------ %%%%

addpath(genpath('~/code/matlab/Atlas_Norm_Dartel_analysis')); 

%% Prerequisites to run DARTEL toolbox. 

% manual alignment
%%% bet images are already aligned. 

% change vox size of AVGT & input images 
% bet images already have the same vox sizes.  

% % execute reslice job. 
% matlabbatch{1}.spm.spatial.coreg.write.ref = {'/home/tchaudhuri/data/Tan_Dartel_Playground/AVGT_x10.nii,1'};
% 
% matlabbatch{1}.spm.spatial.coreg.write.source = {
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0001x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0003x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0005x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0007x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0009x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0011x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0013x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0015x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0017x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0023x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0025x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0029x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0031x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0033x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0035x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0037x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0039x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0041x10__T1w.nii,1'
%                                                  '/home/tchaudhuri/data/Tan_Dartel_Playground/bet_sub-0043x10__T1w.nii,1'
%                                                  };
% 
% matlabbatch{1}.spm.spatial.coreg.write.roptions.interp = 4;
% 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('defaults', 'FMRI');
% spm_jobman('run',matlabbatch);

%% 1. Manual Alignment. 
%%% Align images manually using the display option in SPM. Do not use the
% automated version of this step from ANT-X. 

%% 2. Segmentation using allen space tpms. 
% Segmentation of aligned images. Prerequisite of this is to ensure that
% the input image and the templates have the same resolution. Change voxel
% size using Micha's script.

% addpath(genpath('/home/tchaudhuri/toolboxes/spm12'));
% spm_jobman('initcfg');
% data_dir = input('Enter fullpath of data folder: ');
% cd(data_dir);
% segment_job;
% matlabbatch{1}.spm.spatial.preproc.warp.vox     =  0.7;
% spm_preproc_run(matlabbatch{1}.spm.spatial.preproc,'run')

%  clear matlabbatch
%  
%     matlabbatch{1}.spm.spatial.preproc.channel.vols = {
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0001x10__T1w.nii,1'
%                                                         };
%                                                    %                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0003x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0005x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0007x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0009x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0011x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0013x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0015x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0017x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0023x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0025x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0029x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0031x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0033x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0035x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0037x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0039x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0041x10__T1w.nii,1'
%                                                    '/home/tchaudhuri/data/Tan_Dartel_Playground/rbet_sub-0043x10__T1w.nii,1'
%                                                    };
%     matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 1.0000e-03;
%     matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm = 60;
%     matlabbatch{1}.spm.spatial.preproc.channel.write = [0 1];
%     
%     matlabbatch{1}.spm.spatial.preproc.tissue(1).tpm={'/home/tchaudhuri/data/Tan_Dartel_Playground/_b1grey.nii,1'};
%     matlabbatch{1}.spm.spatial.preproc.tissue(2).tpm={'/home/tchaudhuri/data/Tan_Dartel_Playground/_b2white.nii,1'};
%     matlabbatch{1}.spm.spatial.preproc.tissue(3).tpm={'/home/tchaudhuri/data/Tan_Dartel_Playground/_b3csf.nii,1'};
%     matlabbatch{1}.spm.spatial.preproc.tissue(1).ngaus=1;
%     matlabbatch{1}.spm.spatial.preproc.tissue(2).ngaus=1;
%     matlabbatch{1}.spm.spatial.preproc.tissue(3).ngaus=2;
%     matlabbatch{1}.spm.spatial.preproc.tissue(1).native=[1 1];
%     matlabbatch{1}.spm.spatial.preproc.tissue(2).native=[1 1];
%     matlabbatch{1}.spm.spatial.preproc.tissue(3).native=[1 1];
%     matlabbatch{1}.spm.spatial.preproc.tissue(1).warped=[0 1];
%     matlabbatch{1}.spm.spatial.preproc.tissue(2).warped=[0 1];
%     matlabbatch{1}.spm.spatial.preproc.tissue(3).warped=[0 1];
%     
%     matlabbatch{1}.spm.spatial.preproc.warp.mrf = 1;
%     matlabbatch{1}.spm.spatial.preproc.warp.cleanup = 1;
%     matlabbatch{1}.spm.spatial.preproc.warp.reg = [0 0.0010 0.5000 0.0500 0.2000];
%     matlabbatch{1}.spm.spatial.preproc.warp.affreg = '';
%     matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0;
%     matlabbatch{1}.spm.spatial.preproc.warp.samp = 3;
%     matlabbatch{1}.spm.spatial.preproc.warp.write = [0 0];
%     
%     matlabbatch{1}.spm.spatial.preproc.warp.vox     =  0.7;

%% 2. Segmentation using spmmouse tpms.  - the job below already produces dartel imported images (rc.*), so a separate import step is not needed.

addpath(genpath('/home/tchaudhuri/toolboxes/spm12'));
spm_jobman('initcfg');
clear matlabbatch
segment_en_spmmouse_job; 
spm_preproc_run(matlabbatch{1}.spm.spatial.preproc,'run')

%% 4. Run Dartel (create templates from imported segments) - run only once. For the next run, change template name. 

% create_templates_job; 
% create_templates; 

%% 5. Run Dartel (using existing templates) on affine transformed images (rc1,rc2,...)
% dartel_with_existing_templates_job;
% dartel_with_existing_templates;
 
%% 6. Create Normalised images - create warped images using flow fields (u-files) to get final
% normalised output image. 
% dartel_create_warped_job;
% dartel_create_warped;

%% 7. Evaluating Results 
% --- Qualitative --- %
% Check reg with template image and warped image. 
% template image = Template_6.nii
% warped image = wrc1 

% --- Quantitative --- % [not so sure]
% Convert 4D volume file into a series of 3D volumes. 
% convert_2_3D_job;
% convert_2_3D; 
ref = niftiread('Template_6_00001.nii'); 
A = niftiread('wrc1bet_sub-0001x10__T1w.nii');
[ssimval, ssimmap] = ssim(A,ref);