#!ascii , CsurfColorLUT.txt (put into $CSURF_DIR/lib/lut) ########################################################################## # Annotation regions defined by visual, auditory, and somatomotor maps ########################################################################## # Parcellation drawn on fsaverage using mapping data from: #------------------------------------------------------------------------- # Sood, M. and M.I. Sereno (2016) # Areas activated during naturalistic reading comprehension overlap # topological visual, auditory, and somatotomotor maps. # Human Brain Mapping 37:2784-2810. # https://pages.ucsd.edu/~msereno/papers/LangMaps16.pdf #------------------------------------------------------------------------- # Huang, R.-S. and M.I. Sereno (2013) # Bottom-up retinotopic organization supports top-down mental imagery. # The Open Neuroimaging Journal 7:58-67. # https://pages.ucsd.edu/~msereno/papers/ImaginedNav13.pdf ########################################################################## # Use this file to direct assembly of .annot w/csurf tksurfer write_mgh_annot ########################################################################## ### filename format (for csurf tksurfer) # for each $region name in this file, need matching individual label file # label filename must follow this format (dash '-', not dot '.' after hemi): # ------------------- # $hemi-$region.label # ------------------- ### rules # missing label files are omitted from final annotation # dup region names or colors cause interactive error, write_mgh_annot bail # works for labels from both hemi's (lh-*, rh-*) # if multiple hits at vtx from more than one label, last in this file wins color # alpha here ignored: {U,u}known=>forced to transparent (live-adjust alpha) ### two directives recognized to comment-in/comment-out blocks of regions: # ### exclude_following # ### include_following # N.B.: the first of the 3 hashes must be first char on line to take effect # (so directives can be commented out as above) # the default state without any directives, of course, is show all regions ### HOWTO USE: from tksurfer interface: # ctrl-mid-click "W" on "label:" line to make pop-up # enter MGH-style Color LUT (def: $CSURF_DIR/lib/lut/CsurfColorLUT.txt) # enter output .annot file (def: $subject/label/$hemi.MY_ANNOT.annot) # click READY (OK to skip overlap check) ### HOWTO USE: from tksurfer tcl script: # set lulabel # set anlabel # write_mgh_annot ### HOWTO AVOID: mris_convert crash & freeview errs on write_mgh_annot output: # FreeSurfer utils/colortable.c:CTABreadFromBinaryV1() early req'd seq idnums # FreeSurfer utils/colortable.c:CTABreadFromBinaryV2() allows holes, but buggy # csurf write_mgh_annot() workaround for FreeSurfer bugs: # (1) sequentially re-number region ids to remove holes in list # (2) increment max renum'd region idnum by 1 in header so equals idnum count # This means that region ID nums below will *not* be preserved in output file ########################################################################## #idnum regionname(=labelinfix) R G B A #------------------------------------------------------------------------- ### Any vertex not covered by a label given this region 0 Unknown 0 0 0 0 # ### exclude_following # ### include_following #------------------------------------------------------------------------- ### Visual (100-199) #------------------------------------------------------------------------- ## primary, secondary, tertiary Areas: V1,V2,V3,VP 100 V1_lower 100 0 190 0 101 V1_upper 100 0 200 0 102 V2_lower 60 20 240 0 103 V2_upper 60 20 250 0 104 V3 30 60 200 0 105 VP 30 60 220 0 ## lateral intermediate areas: V3A+, V6, POm, LO's 110 DI 70 100 230 0 111 V3A 10 95 220 0 112 V3B 30 100 250 0 #113 V3C 80 100 180 0 113 OPA 80 100 180 0 114 LO1 90 110 190 0 115 LO2 90 130 150 0 116 LO3 90 120 150 0 117 PGp 90 130 170 0 ## posterior medial areas: V6, V6A, Prostriata 120 V6 35 150 185 0 121 V6A 35 130 195 0 122 aPOS 105 105 185 0 123 POm 110 110 230 0 124 ProS1 80 70 150 0 125 ProS2 90 80 120 0 # lateral temporal areas: MT, MSTd etc, 7b 130 MT_lower 35 175 175 0 131 MT_upper 40 180 180 0 132 MTc 50 140 180 0 133 MSTd 65 130 170 0 134 MSTv 70 150 195 0 135 FSTd 45 120 175 0 136 STV1 45 120 145 0 137 STV2 100 125 145 0 138 7b_PIC 60 155 80 0 # inferior intermediate areas: V4v, V8, fusiform, ventral vis 140 V4v 45 65 245 0 141 hV4 75 75 180 0 142 V8 100 95 205 0 143 PITd 80 90 160 0 144 PH 95 115 160 0 145 FFC 115 125 160 0 146 VVC 125 135 175 0 #147 VMV1 135 75 140 0 147 VO2 135 75 140 0 #148 VMV2 145 95 150 0 148 VO1 145 95 150 0 # superior parietal areas: V7, LIP's, VIP's 150 V7 70 100 220 0 151 cIPS 70 90 170 0 152 LIP0 80 120 230 0 153 LIP1 90 140 240 0 154 PEc 90 160 185 0 #155 SPL1 90 85 205 0 155 IPS5 90 85 205 0 #156 SPL2 100 95 240 0 156 IPS4 100 95 240 0 #157 PCVa 115 75 150 0 157 aPCu1 115 75 150 0 #158 PCVb 145 100 160 0 158 aPCu2 145 100 160 0 # VIP's (divide VIP into vis and multisens, put AIPmult in somato) #160 VIPa 70 170 170 0 160 VIP1vis 70 170 170 0 161 VIP1mult 90 190 100 0 #162 VIPb 50 150 150 0 162 VIP2vis 50 150 150 0 163 VIP2mult 100 200 110 0 ## frontal visual areas (FEF, dmFEF, DLPFC) 170 dmFEF 120 80 210 0 171 FEF 50 200 110 0 172 6a 75 150 100 0 173 DLPFC 125 130 220 0 174 DLPFCa 105 110 190 0 # ### exclude_following # ### include_following #------------------------------------------------------------------------- ### Auditory (200-299) #------------------------------------------------------------------------- # primary-like 200 A1 220 10 20 0 201 R 240 35 60 0 202 RT 250 65 90 0 # posterior belt 203 CM 160 30 80 0 204 CL 190 30 85 0 # medial belt (found 2 not 3, Rauscheker OK w/2!) #210 MBelt1 250 115 100 0 #211 MBelt2 250 135 100 0 #212 MBelt3 250 155 100 0 #210 MB 250 85 65 0 210 MM 250 70 30 0 211 RM 250 95 30 0 ### start Rauscheker renaming, A4a up one level in hierarchy #foreach hemi (lh rh) # mv -i $hemi-LBelt1.label $hemi-ML.label # mv -i $hemi-LBelt2.label $hemi-AL.label # mv -i $hemi-LBelt3.label $hemi-RTL.label # mv -i $hemi-PBelt1.label $hemi-CP.label # mv -i $hemi-PBelt2.label $hemi-MP.label # mv -i $hemi-A4b.label $hemi-AP.label # mv -i $hemi-A5c.label $hemi-RP.label # mv -i $hemi-A4a.label $hemi-C_A4.label # mv -i $hemi-A5a.label $hemi-M_A4.label # mv -i $hemi-A5b.label $hemi-R_A4.label #end # lateral belt #213 LBelt1 240 55 60 0 213 ML 240 55 60 0 #214 LBelt2 240 85 80 0 214 AL 240 85 80 0 #215 LBelt3 240 100 90 0 215 RTL 240 100 90 0 # lateral parabelt, intermed 221 TA2 180 85 90 0 220 TA3 165 65 80 0 #222 PBelt1 250 95 110 0 222 CP 250 95 110 0 #223 PBelt2 250 115 130 0 #223 MP 250 115 130 0 223 MPc 250 115 130 0 # higher-level: A4 #230 A4a 220 125 150 0 230 C_A4 165 115 70 0 #231 A4b 220 135 170 0 #231 AP 220 135 170 0 231 MPr 220 135 170 0 # higher-level: A5 #232 A5a 190 135 85 0 232 M_A4 190 135 85 0 #233 A5b 185 125 65 0 233 R_A4 185 125 65 0 #234 A5c 165 115 70 0 234 RP 220 125 150 0 # STS aud - near VanEssen STPdp/TPOJ1 #240 A6a 150 90 85 0 240 R_A5 150 90 85 0 #242 A6b 140 80 70 0 242 M_A5 140 80 70 0 #next A6c overlaps STVa #241 A6c 110 80 70 0 241 C_A5 110 80 70 0 ### end Rauscheker rename # small auditory area in unactivated genital rep (3a,3b) between hand/foot 250 3aud 230 130 70 0 # subcentral (tympanum area? [here], primary gustatory?) 251 43aud 215 150 70 0 # posterior sylvian (overlaps lg VanEssen PSL=perisylvian language area) 252 PSaud1 240 85 130 0 253 PSaud2 230 105 120 0 # frontal 260 dmFAF 250 125 125 0 261 p32aud 220 95 95 0 #next PZaud overlaps FEF #262 PZaud 200 115 95 0 262 PZa,v,s 190 105 85 0 263 PZa,s 200 115 95 0 #next DLPFCaud overlaps DLPFCa 264 DLPFCaud 210 120 20 0 265 IFSp 180 95 10 0 266 45aud 200 145 20 0 267 FOPaud 220 145 35 0 # ### exclude_following # ### include_following #------------------------------------------------------------------------- ### Somato (300-399) #------------------------------------------------------------------------- # primary #300 3b 301 3b_face 20 200 10 0 302 3b_hand 20 205 10 0 303 3b_foot 20 210 10 0 #304 3a 305 3a_face 40 220 25 0 306 3a_hand 50 230 35 0 307 3a_foot 60 240 45 0 # next not yet divided foot/hand/face #308 1 40 210 40 0 309 1_face 40 210 30 0 310 1_hand 40 215 30 0 311 1_foot 40 225 30 0 312 2 70 255 80 0 #313 2_face #314 2_hand #315 2_foot # dorsal, parietal secondary (PFt mostly foot) 320 5m 70 190 70 0 321 5L 80 170 80 0 322 PFt 100 190 100 0 # Pitzalis posterior cingulate sulcus (vis/leg) 323 pCI 90 160 90 0 # lateral secondary 330 S_II 100 160 45 0 331 PV 120 180 55 0 332 Ig 120 200 75 0 333 FOP2 120 220 75 0 # multisensory 334 AIPmult 70 200 95 0 #------------------------------------------------------------------------- ### Motor (400-499) #------------------------------------------------------------------------- # primary (diag bord moving anterior 3b->4, hand/face border more medial) #400 4 401 4_face 10 190 15 0 402 4_hand 20 190 25 0 403 4_foot 30 190 35 0 #404 4a #405 4a_face #406 4a_hand #407 4a_foot # supplementary motor 410 6d 30 150 35 0 420 SMA1 65 160 60 0 421 SMA2 75 170 70 0