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main_sampleMatching.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Rafael Romero Garcia
%3rd July 2017
%University of Cambridge
%%%%%%%%%%%%%%%INPUT%%%%%%%%%%%%%%%%%%
%Each donor include a parcellation folder (AIBS_map/Allen_FS/donorXXXX/parcellation/) that must contain the file parcellation_name
parcellation_name='500.aparc_dilated_cortical2mm.nii.gz';
%parcellation_name='aparc_dilated_cortical2mm.nii.gz';
%hemiMirror=
%0-Do not mirror samples between hemisphere and consider both hemispheres
%1-Mirror samples and consider only left hemisphere
%2-Mirror samples between hemispheres (left samples are fliped and
%considered in the right hemisphere and viceversa)
hemiMirror=2;1;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
display('Downloading the data and computing the valid probes');
step1_download();
display('Mapping probe to gene');
step2_probe2gene_mapping();
display('Estimating gene expression from probe');
step3_individualProbe_to_geneExpression();
display('Estimate voxels location of each sample in T1 freesurfer space of each donor');
step4_createGeneExpressionTable(hemiMirror);
display('Generate gene expression and coexpression matrices');
step5_interpolateRegions(hemiMirror,parcellation_name);
display('Gene expression matrix created successfully');