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magia_get_freesurfer_roi_info.m
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magia_get_freesurfer_roi_info.m
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function roi_info = magia_get_freesurfer_roi_info(specs)
if(strcmp(specs.magia.roi_set,'tracer_default'))
roi_set = magia_get_tracer_default_roi_set(specs.study.tracer);
else
roi_set = specs.magia.roi_set;
end
switch roi_set
case 'rs1'
roi_info.labels = {'amy' 'cau' 'cer' 'dacc' 'inftemp' 'ins' 'midtemp' 'nacc' 'ofc' 'parsop' 'pcc' 'put' 'racc' 'supfront' 'suptemp' 'tempol' 'tha'};
roi_info.codes = {
[18 54] % amy
[11 50] % cau
[8 47] % cer
[1002 2002] % dacc
[1009 2009] % inftemp
[1035 2035] % ins
[1015 2015] % midtemp
[26 58] % nacc
[1012 1014 2012 2014] % ofc
[1018 2018] % parsop
[1023 2023] % pcc
[12 102 51 111] % put
[1026 2026] % racc
[1028 2028] % supfront
[1030 2030] % suptemp
[1033 2033] % tempol
[9 10 48 49] % tha
};
case 'rs2'
roi_info.labels = {'amy' 'cau' 'cer' 'dacc' 'hip' 'inftemp' 'ins' 'medul' 'midbr' 'midtemp' 'nacc' 'ofc' 'pal' 'parsop' 'pcc' 'pons' 'put' 'racc' 'supfront' 'suptemp' 'tempol' 'tha'};
roi_info.codes = {
[18 54] % amy
[11 50] % cau
[8 47] % cer
[1002 2002] % dacc
[17 53] % hip
[1009 2009] % inftemp
[1035 2035] % ins
[175] % medul
[173] % midbr
[1015 2015] % midtemp
[26 58] % nacc
[1012 1014 2012 2014] % ofc
[13 52] % pal
[1018 2018] % parsop
[1023 2023] % pcc
[174] % pons
[12 102 51 111] % put
[1026 2026] % racc
[1028 2028] % supfront
[1030 2030] % suptemp
[1033 2033] % tempol
[9 10 48 49] % tha
};
case 'rs3'
roi_info.labels = {'amy' 'cau' 'nacc' 'pal' 'put' 'tha'};
roi_info.codes = {
[18 54] % amy
[11 50] % cau
[26 58] % nacc
[13 52] % pal
[12 102 51 111] % put
[9 10 48 49] % tha
};
case 'rs4'
roi_info.labels = {'amy' 'cau' 'dacc' 'hip' 'ins' 'medul' 'midbr' 'nacc' 'oc' 'ofc' 'pal' 'parhip' 'pcc' 'pons' 'put' 'racc' 'tha'};
roi_info.codes = {
[18 54] % amy
[11 50] % cau
[1002 2002] % dacc
[17 53] % hip
[1035 2035] % ins
[175] % medul
[173] % midbr
[26 58] % nacc
[1011 2011] % oc
[1012 1014 2012 2014] % ofc
[13 52] % pal
[1016 2016] % parhip
[1023 2023] % pcc
[174] % pons
[12 102 51 111] % put
[1026 2026] % racc
[9 10 48 49] % tha
};
case 'rs5'
roi_info.labels = {'amy' 'cau' 'dacc' 'hip' 'ins' 'nacc' 'ofc' 'parhip' 'pcc' 'pcun' 'put' 'racc' 'tha'};
roi_info.codes = {
[18 54] % amy
[11 50] % cau
[1002 2002] % dacc
[17 53] % hip
[1035 2035] % ins
[26 58] % nacc
[1012 1014 2012 2014] % ofc
[1016 2016] % parhip
[1023 2023] % pcc
[1025 2025] % pcun
[12 102 51 111] % put
[1026 2026] % racc
[9 10 48 49] % tha
};
case 'rs6'
roi_info.labels = {'CGA' 'CGP' 'LOC' 'LTC' 'MTC' 'PARCALL' 'PIB1PFCALL' 'PIBcomp' 'PREC' 'STR' 'CER'};
roi_info.codes = {
[1002 2002 1026 2026] % anterior cingulate
[1010 2010 1023 2023] % posterior cingulate
[1011 2011] % lateral occipital cortex
[1009 2009 1015 2015 1030 2030 1033 2033 1034 2034] % lateral temporal cortex
[17 53 18 54 1006 2006] % medial temporal cortex
[1008 2008 1029 2029 1031 2031] % parietal cortex
[1003 2003 1012 2012 1014 2014 1018 2018 1019 2019 1020 2020 1027 2027 1028 2028 1032 2032] % prefrontal cortex
[1003 2003 1012 2012 1014 2014 1018 2018 1019 2019 1020 2020 1027 2027 1028 2028 1032 2032 1009 2009 1015 2015 1030 2030 1033 2033 1034 2034 1008 2008 1029 2029 1031 2031 1025 2025 1002 2002 1026 2026 1010 2010 1023 2023] % pibcomp
[1025 2025] % precuneus
[11 50 12 51] % striatum
[8 47] % cerebellum
};
case 'rs7'
roi_info.labels = {'amy' 'cau' 'dacc' 'hip' 'ins' 'nacc' 'oc' 'ofc' 'pal' 'parhip' 'pcc' 'put' 'racc' 'tha'};
roi_info.codes = {
[18 54] % amy
[11 50] % cau
[1002 2002] % dacc
[17 53] % hip
[1035 2035] % ins
[26 58] % nacc
[1012 1014 2012 2014] % ofc
[1011 2011] % oc
[13 52] % pal
[1016 2016] % parhip
[1023 2023] % pcc
[12 102 51 111] % put
[1026 2026] % racc
[9 10 48 49] % tha
};
case 'striat_unil'
roi_info.labels = {'cau_l' 'cau_r' 'nacc_l' 'nacc_r' 'pal_l' 'pal_r' 'put_l' 'put_r' 'tha_l' 'tha_r'};
roi_info.codes = {
11 % cau_l
50 % cau_r
26 % nacc_l
58 % nacc_r
13 % pal_l
52 % pal_r
[12 102] % put_l
[51 111] % put_r
[9 10 ] %tha_l
[48 49] % tha_r
};
case 'rs_CB1R_new'
roi_info.labels = {'amy' 'hip' 'cau' 'put' 'nacc' 'tha' 'cer' 'acc' 'pcc' 'ins' 'ofc' 'suptemp' 'midtemp' 'inftemp' 'supfront' 'midbr' 'pons' 'medul' 'entorhinal' 'pallidum' 'midfront' 'cingulate'};
roi_info.codes = {
[18 54] % amy
[17 53] % hip
[11 50] % cau
[12 102 51 111] % put
[26 58] % nacc
[9 10 48 49] % tha
[8 47] % cer
[1002 2002 1026 2026] % dacc + racc = acc
[1023 2023] % pcc
[1035 2035] % ins
[1012 1014 2012 2014] % ofc
[1030 2030] % suptemp
[1015 2015] % midtemp
[1009 2009] % inftemp
[1028 2028] % supfront
[173] % midbr
[174] % pons
[175] % medul
[1006 2006 ] % entorhinal cortex
[13 52] % pallidum
[1003 1027 2003 2027] % middle frontal
[1002 2002 1026 2026 1023 2023 1010 2010] % cingulate = acc + pcc + isthmus
};
case 'FSlobes'
roi_info.labels = {'fro' 'par' 'tmp' 'occ' 'cin' 'cau' 'put' 'tha' 'hip' 'amy' 'ins' 'pal' 'bs' 'cc' 'cer' 'WM' 'GMctx' 'Brain'}; %see freesurfer cortical lobe parcellation: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
roi_info.codes = {
[ 1028 2028 1027 2027 1003 2003 1018 2018 1020 2020 1019 2019 ...
1014 2014 1012 2012 1024 2024 1017 2017 1032 2032] % frontal lobe
[ 1029 2029 1008 2008 1031 2031 1022 2022 1025 2025 ] %parietal lobe
[ 1009 2009 1015 2015 1030 2030 1001 2001 1007 2007 1034 2034 ...
1006 2006 1033 2033 1016 2016] %temporal lobe
[ 1011 2011 1013 2013 1005 1025 2005 2025 1021 2021 ] %occipital lobe
[ 1002 2002 1026 2026 1010 2010 1023 2023 ] %cingulate (included as a lobe)
[11 50] % cau
[12 102 51 111] % put
[9 10 48 49] % tha
[17 53] % hip
[18 54] % amy
[1035 2035] % ins
[13 52] % pallidum
[16] %brain stem
[251 252 253 254 255] %corpus callosum
[8 47] % cer
[2 41] %cerebral WM
[1000 1001 1002 1003 1005 1006 1007 1008 1009 1010 1011 1012 1013 ...
1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 ...
1028 1029 1030 1031 1032 1033 1034 1035 2000 2001 2002 2003 2005 2006 ...
2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 ...
2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 ...
2035]; %cortical GM
[2 7 8 10 11 12 13 16 17 18 26 28 30 41 46 47 49 50 51 52 53 54 58 60 62 77 80 85 ...
251 252 253 254 255 1000 1001 1002 1003 1005 1006 1007 1008 1009 1010 1011 ...
1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 ...
1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 2000 2001 2002 2003 ...
2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 ...
2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 ...
2033 2034 2035]; %brain
};
otherwise
error('The roi_set %s has not been defined. Please use another roi_set.',roi_set);
end
end