Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

error when running funcroi-table-sess
by suzanne oosterwijk 18 Apr '11

18 Apr '11

Hi Freesurfers, I am trying to run an ROI analysis with a structural and functional constraint in Freesurfer 5 and after I run funcroi-table-sess I get the following error: Parsing the .stats files Building the table.. ERROR: All stat files should have the same segmentations There is also no .dat file created. I am using the following commands: foreach s ( `more sessid` ) mri_cor2label --c $s/mri/aparc+aseg.mgz --id 1035 --l $s/label/lh_insula_aseg.label mri_cor2label --c $s/mri/aparc+aseg.mgz --id 2035 --l $s/label/rh_insula_aseg.label end funcroi-config -roi R_insula_g_mni.roicfg -label rh_insula_aseg -a constr_sm5_mni_gamma_nopace_cor -contrast allvsfix -thresh 2 -sign pos -map sig -fillthresh .5 funcroi-sess -roi R_insula_g_mni.roicfg -sf sessid funcroi-table-sess -roi R_insula_g_mni.roicfg -a constr_sm5_mni_gamma_nopace_cor_extra -c bfvsfix_script -o R_insula_g_mni.bfvsfix_script.dat -sf sessid I have tried many things to see what I am doing wrong, but I can't figure it out. Thanks for any help! Suzanne -- Suzanne Oosterwijk, Ph.D. Postdoctoral Researcher Interdisciplinary Affective Science Lab Department of Psychology Northeastern University 114 Lake Hall s.oosterwijk(a)neu.edu

2 2

Frontal lobes excluded
by Seán Froudist Walsh 18 Apr '11

18 Apr '11

Dear FreeSurfer gurus, I have T1 scans of a patient at three different time-points (one run at each time-point). The cortical reconstructions of the first and third time-points seem to have worked reasonably well, but the reconstruction of the second time-point was a disaster. A massive part of the frontal lobe (bilaterally) is cut out from the wm and gm surfaces. I tried fixing this with wm edits, but that exited with errors, then I tried to add control points to the new wm.mgz and recon-all again exited with errors. Is there any possibility of saving this scan? Would I be able to upload some screenshots to help you see what is going on? Many thanks in advance, Sean

2 1

Pial surface error
by Allie Rosen 18 Apr '11

18 Apr '11

Hi, Once processed, several of my subjects have had errors around the occipital lobe. Attached is an example. I've already tried editing brainmask.mgz and running recon-all, but as you can see, this didn't change the pial or wm borders. What can I do to fix this? Thank you, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

2 1

gray/white/other with mri_segstats with version 5stable
by Saad Ramadan 18 Apr '11

18 Apr '11

Hi , When I do mri_segstats, about 1200 "segmentation ids" are produced with some of them having vague names (at least for me). Pls find below a typical output (around 1200 lines) or mri_segstats. The commad I use is: mri_segstats --seg $SUBJECTS_DIR/subject/mri/aparc+aseg.mgz --ctab-default --i svs.anat.nii --mask svs.anat.nii --sum svs.summary.dat My desired output would contain (1) how many voxels of gray matter I have, (2) white matter and (3) other of CSF. Presently, I have to go through the output line by line, and classify each item as gray. white. or csf and then do the sums in the end. Is there a way to obtain a simplified output like the one I described above? Thank you 0 0 Unknown 16769446 1.67694e+07 1 1 Left-Cerebral-Exterior 0 2 2 Left-Cerebral-White-Matter 5867 5867 3 3 Left-Cerebral-Cortex 0 4 4 Left-Lateral-Ventricle 30 30 5 5 Left-Inf-Lat-Vent 0 6 6 Left-Cerebellum-Exterior 0 7 7 Left-Cerebellum-White-Matter 0 8 8 Left-Cerebellum-Cortex 0 9 9 Left-Thalamus 0 10 10 Left-Thalamus-Proper 0 11 11 Left-Caudate 196 196 12 12 Left-Putamen 0 13 13 Left-Pallidum 0 14 14 3rd-Ventricle 0 15 15 4th-Ventricle 0 16 16 Brain-Stem 0 17 17 Left-Hippocampus 0 18 18 Left-Amygdala 0 19 19 Left-Insula 0 20 20 Left-Operculum 0 21 21 Line-1 0 22 22 Line-2 0 23 23 Line-3 0 24 24 CSF 0 25 25 Left-Lesion 0 26 26 Left-Accumbens-area 0 27 27 Left-Substancia-Nigra 0 28 28 Left-VentralDC 0 29 29 Left-undetermined 0 30 30 Left-vessel 0 31 31 Left-choroid-plexus 2 2 32 32 Left-F3orb 0 33 33 Left-lOg 0 34 34 Left-aOg 0 35 35 Left-mOg 0 36 36 Left-pOg 0 37 37 Left-Stellate 0 38 38 Left-Porg 0 39 39 Left-Aorg 0 40 40 Right-Cerebral-Exterior 0 41 41 Right-Cerebral-White-Matter 0 42 42 Right-Cerebral-Cortex 0 43 43 Right-Lateral-Ventricle 0 44 44 Right-Inf-Lat-Vent 0 45 45 Right-Cerebellum-Exterior 0 46 46 Right-Cerebellum-White-Matter 0 47 47 Right-Cerebellum-Cortex 0 48 48 Right-Thalamus 0 49 49 Right-Thalamus-Proper 0 50 50 Right-Caudate 0 51 51 Right-Putamen 0 52 52 Right-Pallidum 0 53 53 Right-Hippocampus 0 54 54 Right-Amygdala 0 55 55 Right-Insula 0 56 56 Right-Operculum 0 57 57 Right-Lesion 0 58 58 Right-Accumbens-area 0 59 59 Right-Substancia-Nigra 0 60 60 Right-VentralDC 0 61 61 Right-undetermined 0 62 62 Right-vessel 0 63 63 Right-choroid-plexus 0 64 64 Right-F3orb 0 65 65 Right-lOg 0 66 66 Right-aOg 0 67 67 Right-mOg 0 68 68 Right-pOg 0 69 69 Right-Stellate 0 70 70 Right-Porg 0 71 71 Right-Aorg 0 72 72 5th-Ventricle 0 73 73 Left-Interior 0 74 74 Right-Interior 0 75 75 Left-Lateral-Ventricles 0 76 76 Right-Lateral-Ventricles 0 77 77 WM-hypointensities 87 87 78 78 Left-WM-hypointensities 0 79 79 Right-WM-hypointensities 0 80 80 non-WM-hypointensities 0 81 81 Left-non-WM-hypointensities 0 82 82 Right-non-WM-hypointensities 0 83 83 Left-F1 0 84 84 Right-F1 0 85 85 Optic-Chiasm 0 86 86 Corpus_Callosum 0 87 96 Left-Amygdala-Anterior 0 88 97 Right-Amygdala-Anterior 0 89 98 Dura 0 90 100 Left-wm-intensity-abnormality 0 91 101 Left-caudate-intensity-abnormality 0 92 102 Left-putamen-intensity-abnormality 0 93 103 Left-accumbens-intensity-abnormality 0 94 104 Left-pallidum-intensity-abnormality 0 95 105 Left-amygdala-intensity-abnormality 0 96 106 Left-hippocampus-intensity-abnormality 0 97 107 Left-thalamus-intensity-abnormality 0 98 108 Left-VDC-intensity-abnormality 0 99 109 Right-wm-intensity-abnormality 0 100 110 Right-caudate-intensity-abnormality 0 101 111 Right-putamen-intensity-abnormality 0 102 112 Right-accumbens-intensity-abnormality 0 103 113 Right-pallidum-intensity-abnormality 0 104 114 Right-amygdala-intensity-abnormality 0 105 115 Right-hippocampus-intensity-abnormality 0 106 116 Right-thalamus-intensity-abnormality 0 107 117 Right-VDC-intensity-abnormality 0 108 118 Epidermis 0 109 119 Conn-Tissue 0 110 120 SC-Fat/Muscle 0 111 121 Cranium 0 112 122 CSF-SA 0 113 123 Muscle 0 114 124 Ear 0 115 125 Adipose 0 116 126 Spinal-Cord 0 117 127 Soft-Tissue 0 118 128 Nerve 0 119 129 Bone 0 120 130 Air 0 121 131 Orbital-Fat 0 122 132 Tongue 0 123 133 Nasal-Structures 0 124 134 Globe 0 125 135 Teeth 0 126 136 Left-Caudate/Putamen 0 127 137 Right-Caudate/Putamen 0 128 138 Left-Claustrum 0 129 139 Right-Claustrum 0 130 140 Cornea 0 131 142 Diploe 0 132 143 Vitreous-Humor 0 133 144 Lens 0 134 145 Aqueous-Humor 0 135 146 Outer-Table 0 136 147 Inner-Table 0 137 148 Periosteum 0 138 149 Endosteum 0 139 150 R/C/S 0 140 151 Iris 0 141 152 SC-Adipose/Muscle 0 142 153 SC-Tissue 0 143 154 Orbital-Adipose 0 144 155 Left-IntCapsule-Ant 0 145 156 Right-IntCapsule-Ant 0 146 157 Left-IntCapsule-Pos 0 147 158 Right-IntCapsule-Pos 0 148 159 Left-Cerebral-WM-unmyelinated 0 149 160 Right-Cerebral-WM-unmyelinated 0 150 161 Left-Cerebral-WM-myelinated 0 151 162 Right-Cerebral-WM-myelinated 0 152 163 Left-Subcortical-Gray-Matter 0 153 164 Right-Subcortical-Gray-Matter 0 154 165 Skull 0 155 166 Posterior-fossa 0 156 167 Scalp 0 157 168 Hematoma 0 158 180 Left-Cortical-Dysplasia 0 159 181 Right-Cortical-Dysplasia 0 160 193 Left-hippocampal_fissure 0 161 194 Left-CADG-head 0 162 195 Left-subiculum 0 163 196 Left-fimbria 0 164 197 Right-hippocampal_fissure 0 165 198 Right-CADG-head 0 166 199 Right-subiculum 0 167 200 Right-fimbria 0 168 201 alveus 0 169 202 perforant_pathway 0 170 203 parasubiculum 0 171 204 presubiculum 0 172 205 subiculum 0 173 206 CA1 0 174 207 CA2 0 175 208 CA3 0 176 209 CA4 0 177 210 GC-DG 0 178 211 HATA 0 179 212 fimbria 0 180 213 lateral_ventricle 0 181 214 molecular_layer_HP 0 182 215 hippocampal_fissure 0 183 216 entorhinal_cortex 0 184 217 molecular_layer_subiculum 0 185 218 Amygdala 0 186 219 Cerebral_White_Matter 0 187 220 Cerebral_Cortex 0 188 221 Inf_Lat_Vent 0 189 222 Perirhinal 0 190 223 Cerebral_White_Matter_Edge 0 191 224 Background 0 192 225 Ectorhinal 0 193 250 Fornix 0 194 251 CC_Posterior 0 195 252 CC_Mid_Posterior 0 196 253 CC_Central 0 197 254 CC_Mid_Anterior 0 198 255 CC_Anterior 0 199 256 Voxel-Unchanged 0 200 331 Aorta 0 201 332 Left-Common-IliacA 0 202 333 Right-Common-IliacA 0 203 334 Left-External-IliacA 0 204 335 Right-External-IliacA 0 205 336 Left-Internal-IliacA 0 206 337 Right-Internal-IliacA 0 207 338 Left-Lateral-SacralA 0 208 339 Right-Lateral-SacralA 0 209 340 Left-ObturatorA 0 210 341 Right-ObturatorA 0 211 342 Left-Internal-PudendalA 0 212 343 Right-Internal-PudendalA 0 213 344 Left-UmbilicalA 0 214 345 Right-UmbilicalA 0 215 346 Left-Inf-RectalA 0 216 347 Right-Inf-RectalA 0 217 348 Left-Common-IliacV 0 218 349 Right-Common-IliacV 0 219 350 Left-External-IliacV 0 220 351 Right-External-IliacV 0 221 352 Left-Internal-IliacV 0 222 353 Right-Internal-IliacV 0 223 354 Left-ObturatorV 0 224 355 Right-ObturatorV 0 225 356 Left-Internal-PudendalV 0 226 357 Right-Internal-PudendalV 0 227 358 Pos-Lymph 0 228 359 Neg-Lymph 0 229 400 V1 0 230 401 V2 0 231 402 BA44 0 232 403 BA45 0 233 404 BA4a 0 234 405 BA4p 0 235 406 BA6 0 236 407 BA2 0 237 408 BA1_old 0 238 409 BAun2 0 239 410 BA1 0 240 411 BA2b 0 241 412 BA3a 0 242 413 BA3b 0 243 414 MT 0 244 415 AIPS_AIP_l 0 245 416 AIPS_AIP_r 0 246 417 AIPS_VIP_l 0 247 418 AIPS_VIP_r 0 248 419 IPL_PFcm_l 0 249 420 IPL_PFcm_r 0 250 421 IPL_PF_l 0 251 422 IPL_PFm_l 0 252 423 IPL_PFm_r 0 253 424 IPL_PFop_l 0 254 425 IPL_PFop_r 0 255 426 IPL_PF_r 0 256 427 IPL_PFt_l 0 257 428 IPL_PFt_r 0 258 429 IPL_PGa_l 0 259 430 IPL_PGa_r 0 260 431 IPL_PGp_l 0 261 432 IPL_PGp_r 0 262 433 Visual_V3d_l 0 263 434 Visual_V3d_r 0 264 435 Visual_V4_l 0 265 436 Visual_V4_r 0 266 437 Visual_V5_b 0 267 438 Visual_VP_l 0 268 439 Visual_VP_r 0 269 500 right_CA2/3 0 270 501 right_alveus 0 271 502 right_CA1 0 272 503 right_fimbria 0 273 504 right_presubiculum 0 274 505 right_hippocampal_fissure 0 275 506 right_CA4/DG 0 276 507 right_subiculum 0 277 508 right_fornix 0 278 550 left_CA2/3 0 279 551 left_alveus 0 280 552 left_CA1 0 281 553 left_fimbria 0 282 554 left_presubiculum 0 283 555 left_hippocampal_fissure 0 284 556 left_CA4/DG 0 285 557 left_subiculum 0 286 558 left_fornix 0 287 600 Tumor 0 288 701 CSF-FSL-FAST 0 289 702 GrayMatter-FSL-FAST 0 290 703 WhiteMatter-FSL-FAST 0 291 999 SUSPICIOUS 0 292 1000 ctx-lh-unknown 0 293 1001 ctx-lh-bankssts 0 294 1002 ctx-lh-caudalanteriorcingulate 0 295 1003 ctx-lh-caudalmiddlefrontal 0 296 1004 ctx-lh-corpuscallosum 0 297 1005 ctx-lh-cuneus 0 298 1006 ctx-lh-entorhinal 0 299 1007 ctx-lh-fusiform 0 300 1008 ctx-lh-inferiorparietal 0 301 1009 ctx-lh-inferiortemporal 0 302 1010 ctx-lh-isthmuscingulate 0 303 1011 ctx-lh-lateraloccipital 0 304 1012 ctx-lh-lateralorbitofrontal 129 129 305 1013 ctx-lh-lingual 0 306 1014 ctx-lh-medialorbitofrontal 0 307 1015 ctx-lh-middletemporal 0 308 1016 ctx-lh-parahippocampal 0 309 1017 ctx-lh-paracentral 0 310 1018 ctx-lh-parsopercularis 226 226 311 1019 ctx-lh-parsorbitalis 0 312 1020 ctx-lh-parstriangularis 478 478 313 1021 ctx-lh-pericalcarine 0 314 1022 ctx-lh-postcentral 0 315 1023 ctx-lh-posteriorcingulate 0 316 1024 ctx-lh-precentral 0 317 1025 ctx-lh-precuneus 0 318 1026 ctx-lh-rostralanteriorcingulate 0 319 1027 ctx-lh-rostralmiddlefrontal 412 412 320 1028 ctx-lh-superiorfrontal 3 3 321 1029 ctx-lh-superiorparietal 0 322 1030 ctx-lh-superiortemporal 0 323 1031 ctx-lh-supramarginal 0 324 1032 ctx-lh-frontalpole 0 325 1033 ctx-lh-temporalpole 0 326 1034 ctx-lh-transversetemporal 0 327 1035 ctx-lh-insula 340 340 328 1100 ctx-lh-Unknown 0 329 1101 ctx-lh-Corpus_callosum 0 330 1102 ctx-lh-G_and_S_Insula_ONLY_AVERAGE 0 331 1103 ctx-lh-G_cingulate-Isthmus 0 332 1104 ctx-lh-G_cingulate-Main_part 0 333 1105 ctx-lh-G_cuneus 0 334 1106 ctx-lh-G_frontal_inf-Opercular_part 0 335 1107 ctx-lh-G_frontal_inf-Orbital_part 0 336 1108 ctx-lh-G_frontal_inf-Triangular_part 0 337 1109 ctx-lh-G_frontal_middle 0 338 1110 ctx-lh-G_frontal_superior 0 339 1111 ctx-lh-G_frontomarginal 0 340 1112 ctx-lh-G_insular_long 0 341 1113 ctx-lh-G_insular_short 0 342 1114 ctx-lh-G_and_S_occipital_inferior 0 343 1115 ctx-lh-G_occipital_middle 0 344 1116 ctx-lh-G_occipital_superior 0 345 1117 ctx-lh-G_occipit-temp_lat-Or_fusiform 0 346 1118 ctx-lh-G_occipit-temp_med-Lingual_part 0 347 1119 ctx-lh-G_occipit-temp_med-Parahippocampal_part 0 348 1120 ctx-lh-G_orbital 0 349 1121 ctx-lh-G_paracentral 0 350 1122 ctx-lh-G_parietal_inferior-Angular_part 0 351 1123 ctx-lh-G_parietal_inferior-Supramarginal_part 0 352 1124 ctx-lh-G_parietal_superior 0 353 1125 ctx-lh-G_postcentral 0 354 1126 ctx-lh-G_precentral 0 355 1127 ctx-lh-G_precuneus 0 356 1128 ctx-lh-G_rectus 0 357 1129 ctx-lh-G_subcallosal 0 358 1130 ctx-lh-G_subcentral 0 359 1131 ctx-lh-G_temporal_inferior 0 360 1132 ctx-lh-G_temporal_middle 0 361 1133 ctx-lh-G_temp_sup-G_temp_transv_and_interm_S 0 362 1134 ctx-lh-G_temp_sup-Lateral_aspect 0 363 1135 ctx-lh-G_temp_sup-Planum_polare 0 364 1136 ctx-lh-G_temp_sup-Planum_tempolare 0 365 1137 ctx-lh-G_and_S_transverse_frontopolar 0 366 1138 ctx-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 367 1139 ctx-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 368 1140 ctx-lh-Lat_Fissure-post_sgt 0 369 1141 ctx-lh-Medial_wall 0 370 1142 ctx-lh-Pole_occipital 0 371 1143 ctx-lh-Pole_temporal 0 372 1144 ctx-lh-S_calcarine 0 373 1145 ctx-lh-S_central 0 374 1146 ctx-lh-S_central_insula 0 375 1147 ctx-lh-S_cingulate-Main_part_and_Intracingulate 0 376 1148 ctx-lh-S_cingulate-Marginalis_part 0 377 1149 ctx-lh-S_circular_insula_anterior 0 378 1150 ctx-lh-S_circular_insula_inferior 0 379 1151 ctx-lh-S_circular_insula_superior 0 380 1152 ctx-lh-S_collateral_transverse_ant 0 381 1153 ctx-lh-S_collateral_transverse_post 0 382 1154 ctx-lh-S_frontal_inferior 0 383 1155 ctx-lh-S_frontal_middle 0 384 1156 ctx-lh-S_frontal_superior 0 385 1157 ctx-lh-S_frontomarginal 0 386 1158 ctx-lh-S_intermedius_primus-Jensen 0 387 1159 ctx-lh-S_intraparietal-and_Parietal_transverse 0 388 1160 ctx-lh-S_occipital_anterior 0 389 1161 ctx-lh-S_occipital_middle_and_Lunatus 0 390 1162 ctx-lh-S_occipital_superior_and_transversalis 0 391 1163 ctx-lh-S_occipito-temporal_lateral 0 392 1164 ctx-lh-S_occipito-temporal_medial_and_S_Lingual 0 393 1165 ctx-lh-S_orbital-H_shapped 0 394 1166 ctx-lh-S_orbital_lateral 0 395 1167 ctx-lh-S_orbital_medial-Or_olfactory 0 396 1168 ctx-lh-S_paracentral 0 397 1169 ctx-lh-S_parieto_occipital 0 398 1170 ctx-lh-S_pericallosal 0 399 1171 ctx-lh-S_postcentral 0 400 1172 ctx-lh-S_precentral-Inferior-part 0 401 1173 ctx-lh-S_precentral-Superior-part 0 402 1174 ctx-lh-S_subcentral_ant 0 403 1175 ctx-lh-S_subcentral_post 0 404 1176 ctx-lh-S_suborbital 0 405 1177 ctx-lh-S_subparietal 0 406 1178 ctx-lh-S_supracingulate 0 407 1179 ctx-lh-S_temporal_inferior 0 408 1180 ctx-lh-S_temporal_superior 0 409 1181 ctx-lh-S_temporal_transverse 0 410 1200 ctx-lh-G_cingulate-caudal_ACC 0 411 1201 ctx-lh-G_cingulate-rostral_ACC 0 412 1202 ctx-lh-G_cingulate-posterior 0 413 1205 ctx-lh-S_cingulate-caudal_ACC 0 414 1206 ctx-lh-S_cingulate-rostral_ACC 0 415 1207 ctx-lh-S_cingulate-posterior 0 416 1210 ctx-lh-S_pericallosal-caudal 0 417 1211 ctx-lh-S_pericallosal-rostral 0 418 1212 ctx-lh-S_pericallosal-posterior 0 419 2000 ctx-rh-unknown 0 420 2001 ctx-rh-bankssts 0 421 2002 ctx-rh-caudalanteriorcingulate 0 422 2003 ctx-rh-caudalmiddlefrontal 0 423 2004 ctx-rh-corpuscallosum 0 424 2005 ctx-rh-cuneus 0 425 2006 ctx-rh-entorhinal 0 426 2007 ctx-rh-fusiform 0 427 2008 ctx-rh-inferiorparietal 0 428 2009 ctx-rh-inferiortemporal 0 429 2010 ctx-rh-isthmuscingulate 0 430 2011 ctx-rh-lateraloccipital 0 431 2012 ctx-rh-lateralorbitofrontal 0 432 2013 ctx-rh-lingual 0 433 2014 ctx-rh-medialorbitofrontal 0 434 2015 ctx-rh-middletemporal 0 435 2016 ctx-rh-parahippocampal 0 436 2017 ctx-rh-paracentral 0 437 2018 ctx-rh-parsopercularis 0 438 2019 ctx-rh-parsorbitalis 0 439 2020 ctx-rh-parstriangularis 0 440 2021 ctx-rh-pericalcarine 0 441 2022 ctx-rh-postcentral 0 442 2023 ctx-rh-posteriorcingulate 0 443 2024 ctx-rh-precentral 0 444 2025 ctx-rh-precuneus 0 445 2026 ctx-rh-rostralanteriorcingulate 0 446 2027 ctx-rh-rostralmiddlefrontal 0 447 2028 ctx-rh-superiorfrontal 0 448 2029 ctx-rh-superiorparietal 0 449 2030 ctx-rh-superiortemporal 0 450 2031 ctx-rh-supramarginal 0 451 2032 ctx-rh-frontalpole 0 452 2033 ctx-rh-temporalpole 0 453 2034 ctx-rh-transversetemporal 0 454 2035 ctx-rh-insula 0 455 2100 ctx-rh-Unknown 0 456 2101 ctx-rh-Corpus_callosum 0 457 2102 ctx-rh-G_and_S_Insula_ONLY_AVERAGE 0 458 2103 ctx-rh-G_cingulate-Isthmus 0 459 2104 ctx-rh-G_cingulate-Main_part 0 460 2105 ctx-rh-G_cuneus 0 461 2106 ctx-rh-G_frontal_inf-Opercular_part 0 462 2107 ctx-rh-G_frontal_inf-Orbital_part 0 463 2108 ctx-rh-G_frontal_inf-Triangular_part 0 464 2109 ctx-rh-G_frontal_middle 0 465 2110 ctx-rh-G_frontal_superior 0 466 2111 ctx-rh-G_frontomarginal 0 467 2112 ctx-rh-G_insular_long 0 468 2113 ctx-rh-G_insular_short 0 469 2114 ctx-rh-G_and_S_occipital_inferior 0 470 2115 ctx-rh-G_occipital_middle 0 471 2116 ctx-rh-G_occipital_superior 0 472 2117 ctx-rh-G_occipit-temp_lat-Or_fusiform 0 473 2118 ctx-rh-G_occipit-temp_med-Lingual_part 0 474 2119 ctx-rh-G_occipit-temp_med-Parahippocampal_part 0 475 2120 ctx-rh-G_orbital 0 476 2121 ctx-rh-G_paracentral 0 477 2122 ctx-rh-G_parietal_inferior-Angular_part 0 478 2123 ctx-rh-G_parietal_inferior-Supramarginal_part 0 479 2124 ctx-rh-G_parietal_superior 0 480 2125 ctx-rh-G_postcentral 0 481 2126 ctx-rh-G_precentral 0 482 2127 ctx-rh-G_precuneus 0 483 2128 ctx-rh-G_rectus 0 484 2129 ctx-rh-G_subcallosal 0 485 2130 ctx-rh-G_subcentral 0 486 2131 ctx-rh-G_temporal_inferior 0 487 2132 ctx-rh-G_temporal_middle 0 488 2133 ctx-rh-G_temp_sup-G_temp_transv_and_interm_S 0 489 2134 ctx-rh-G_temp_sup-Lateral_aspect 0 490 2135 ctx-rh-G_temp_sup-Planum_polare 0 491 2136 ctx-rh-G_temp_sup-Planum_tempolare 0 492 2137 ctx-rh-G_and_S_transverse_frontopolar 0 493 2138 ctx-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 494 2139 ctx-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 495 2140 ctx-rh-Lat_Fissure-post_sgt 0 496 2141 ctx-rh-Medial_wall 0 497 2142 ctx-rh-Pole_occipital 0 498 2143 ctx-rh-Pole_temporal 0 499 2144 ctx-rh-S_calcarine 0 500 2145 ctx-rh-S_central 0 501 2146 ctx-rh-S_central_insula 0 502 2147 ctx-rh-S_cingulate-Main_part_and_Intracingulate 0 503 2148 ctx-rh-S_cingulate-Marginalis_part 0 504 2149 ctx-rh-S_circular_insula_anterior 0 505 2150 ctx-rh-S_circular_insula_inferior 0 506 2151 ctx-rh-S_circular_insula_superior 0 507 2152 ctx-rh-S_collateral_transverse_ant 0 508 2153 ctx-rh-S_collateral_transverse_post 0 509 2154 ctx-rh-S_frontal_inferior 0 510 2155 ctx-rh-S_frontal_middle 0 511 2156 ctx-rh-S_frontal_superior 0 512 2157 ctx-rh-S_frontomarginal 0 513 2158 ctx-rh-S_intermedius_primus-Jensen 0 514 2159 ctx-rh-S_intraparietal-and_Parietal_transverse 0 515 2160 ctx-rh-S_occipital_anterior 0 516 2161 ctx-rh-S_occipital_middle_and_Lunatus 0 517 2162 ctx-rh-S_occipital_superior_and_transversalis 0 518 2163 ctx-rh-S_occipito-temporal_lateral 0 519 2164 ctx-rh-S_occipito-temporal_medial_and_S_Lingual 0 520 2165 ctx-rh-S_orbital-H_shapped 0 521 2166 ctx-rh-S_orbital_lateral 0 522 2167 ctx-rh-S_orbital_medial-Or_olfactory 0 523 2168 ctx-rh-S_paracentral 0 524 2169 ctx-rh-S_parieto_occipital 0 525 2170 ctx-rh-S_pericallosal 0 526 2171 ctx-rh-S_postcentral 0 527 2172 ctx-rh-S_precentral-Inferior-part 0 528 2173 ctx-rh-S_precentral-Superior-part 0 529 2174 ctx-rh-S_subcentral_ant 0 530 2175 ctx-rh-S_subcentral_post 0 531 2176 ctx-rh-S_suborbital 0 532 2177 ctx-rh-S_subparietal 0 533 2178 ctx-rh-S_supracingulate 0 534 2179 ctx-rh-S_temporal_inferior 0 535 2180 ctx-rh-S_temporal_superior 0 536 2181 ctx-rh-S_temporal_transverse 0 537 2200 ctx-rh-G_cingulate-caudal_ACC 0 538 2201 ctx-rh-G_cingulate-rostral_ACC 0 539 2202 ctx-rh-G_cingulate-posterior 0 540 2205 ctx-rh-S_cingulate-caudal_ACC 0 541 2206 ctx-rh-S_cingulate-rostral_ACC 0 542 2207 ctx-rh-S_cingulate-posterior 0 543 2210 ctx-rh-S_pericallosal-caudal 0 544 2211 ctx-rh-S_pericallosal-rostral 0 545 2212 ctx-rh-S_pericallosal-posterior 0 546 3000 wm-lh-unknown 0 547 3001 wm-lh-bankssts 0 548 3002 wm-lh-caudalanteriorcingulate 0 549 3003 wm-lh-caudalmiddlefrontal 0 550 3004 wm-lh-corpuscallosum 0 551 3005 wm-lh-cuneus 0 552 3006 wm-lh-entorhinal 0 553 3007 wm-lh-fusiform 0 554 3008 wm-lh-inferiorparietal 0 555 3009 wm-lh-inferiortemporal 0 556 3010 wm-lh-isthmuscingulate 0 557 3011 wm-lh-lateraloccipital 0 558 3012 wm-lh-lateralorbitofrontal 0 559 3013 wm-lh-lingual 0 560 3014 wm-lh-medialorbitofrontal 0 561 3015 wm-lh-middletemporal 0 562 3016 wm-lh-parahippocampal 0 563 3017 wm-lh-paracentral 0 564 3018 wm-lh-parsopercularis 0 565 3019 wm-lh-parsorbitalis 0 566 3020 wm-lh-parstriangularis 0 567 3021 wm-lh-pericalcarine 0 568 3022 wm-lh-postcentral 0 569 3023 wm-lh-posteriorcingulate 0 570 3024 wm-lh-precentral 0 571 3025 wm-lh-precuneus 0 572 3026 wm-lh-rostralanteriorcingulate 0 573 3027 wm-lh-rostralmiddlefrontal 0 574 3028 wm-lh-superiorfrontal 0 575 3029 wm-lh-superiorparietal 0 576 3030 wm-lh-superiortemporal 0 577 3031 wm-lh-supramarginal 0 578 3032 wm-lh-frontalpole 0 579 3033 wm-lh-temporalpole 0 580 3034 wm-lh-transversetemporal 0 581 3035 wm-lh-insula 0 582 3100 wm-lh-Unknown 0 583 3101 wm-lh-Corpus_callosum 0 584 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 585 3103 wm-lh-G_cingulate-Isthmus 0 586 3104 wm-lh-G_cingulate-Main_part 0 587 3105 wm-lh-G_cuneus 0 588 3106 wm-lh-G_frontal_inf-Opercular_part 0 589 3107 wm-lh-G_frontal_inf-Orbital_part 0 590 3108 wm-lh-G_frontal_inf-Triangular_part 0 591 3109 wm-lh-G_frontal_middle 0 592 3110 wm-lh-G_frontal_superior 0 593 3111 wm-lh-G_frontomarginal 0 594 3112 wm-lh-G_insular_long 0 595 3113 wm-lh-G_insular_short 0 596 3114 wm-lh-G_and_S_occipital_inferior 0 597 3115 wm-lh-G_occipital_middle 0 598 3116 wm-lh-G_occipital_superior 0 599 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 600 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 601 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 602 3120 wm-lh-G_orbital 0 603 3121 wm-lh-G_paracentral 0 604 3122 wm-lh-G_parietal_inferior-Angular_part 0 605 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 606 3124 wm-lh-G_parietal_superior 0 607 3125 wm-lh-G_postcentral 0 608 3126 wm-lh-G_precentral 0 609 3127 wm-lh-G_precuneus 0 610 3128 wm-lh-G_rectus 0 611 3129 wm-lh-G_subcallosal 0 612 3130 wm-lh-G_subcentral 0 613 3131 wm-lh-G_temporal_inferior 0 614 3132 wm-lh-G_temporal_middle 0 615 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 616 3134 wm-lh-G_temp_sup-Lateral_aspect 0 617 3135 wm-lh-G_temp_sup-Planum_polare 0 618 3136 wm-lh-G_temp_sup-Planum_tempolare 0 619 3137 wm-lh-G_and_S_transverse_frontopolar 0 620 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 621 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 622 3140 wm-lh-Lat_Fissure-post_sgt 0 623 3141 wm-lh-Medial_wall 0 624 3142 wm-lh-Pole_occipital 0 625 3143 wm-lh-Pole_temporal 0 626 3144 wm-lh-S_calcarine 0 627 3145 wm-lh-S_central 0 628 3146 wm-lh-S_central_insula 0 629 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 630 3148 wm-lh-S_cingulate-Marginalis_part 0 631 3149 wm-lh-S_circular_insula_anterior 0 632 3150 wm-lh-S_circular_insula_inferior 0 633 3151 wm-lh-S_circular_insula_superior 0 634 3152 wm-lh-S_collateral_transverse_ant 0 635 3153 wm-lh-S_collateral_transverse_post 0 636 3154 wm-lh-S_frontal_inferior 0 637 3155 wm-lh-S_frontal_middle 0 638 3156 wm-lh-S_frontal_superior 0 639 3157 wm-lh-S_frontomarginal 0 640 3158 wm-lh-S_intermedius_primus-Jensen 0 641 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 642 3160 wm-lh-S_occipital_anterior 0 643 3161 wm-lh-S_occipital_middle_and_Lunatus 0 644 3162 wm-lh-S_occipital_superior_and_transversalis 0 645 3163 wm-lh-S_occipito-temporal_lateral 0 646 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 647 3165 wm-lh-S_orbital-H_shapped 0 648 3166 wm-lh-S_orbital_lateral 0 649 3167 wm-lh-S_orbital_medial-Or_olfactory 0 650 3168 wm-lh-S_paracentral 0 651 3169 wm-lh-S_parieto_occipital 0 652 3170 wm-lh-S_pericallosal 0 653 3171 wm-lh-S_postcentral 0 654 3172 wm-lh-S_precentral-Inferior-part 0 655 3173 wm-lh-S_precentral-Superior-part 0 656 3174 wm-lh-S_subcentral_ant 0 657 3175 wm-lh-S_subcentral_post 0 658 3176 wm-lh-S_suborbital 0 659 3177 wm-lh-S_subparietal 0 660 3178 wm-lh-S_supracingulate 0 661 3179 wm-lh-S_temporal_inferior 0 662 3180 wm-lh-S_temporal_superior 0 663 3181 wm-lh-S_temporal_transverse 0 664 4000 wm-rh-unknown 0 665 4001 wm-rh-bankssts 0 666 4002 wm-rh-caudalanteriorcingulate 0 667 4003 wm-rh-caudalmiddlefrontal 0 668 4004 wm-rh-corpuscallosum 0 669 4005 wm-rh-cuneus 0 670 4006 wm-rh-entorhinal 0 671 4007 wm-rh-fusiform 0 672 4008 wm-rh-inferiorparietal 0 673 4009 wm-rh-inferiortemporal 0 674 4010 wm-rh-isthmuscingulate 0 675 4011 wm-rh-lateraloccipital 0 676 4012 wm-rh-lateralorbitofrontal 0 677 4013 wm-rh-lingual 0 678 4014 wm-rh-medialorbitofrontal 0 679 4015 wm-rh-middletemporal 0 680 4016 wm-rh-parahippocampal 0 681 4017 wm-rh-paracentral 0 682 4018 wm-rh-parsopercularis 0 683 4019 wm-rh-parsorbitalis 0 684 4020 wm-rh-parstriangularis 0 685 4021 wm-rh-pericalcarine 0 686 4022 wm-rh-postcentral 0 687 4023 wm-rh-posteriorcingulate 0 688 4024 wm-rh-precentral 0 689 4025 wm-rh-precuneus 0 690 4026 wm-rh-rostralanteriorcingulate 0 691 4027 wm-rh-rostralmiddlefrontal 0 692 4028 wm-rh-superiorfrontal 0 693 4029 wm-rh-superiorparietal 0 694 4030 wm-rh-superiortemporal 0 695 4031 wm-rh-supramarginal 0 696 4032 wm-rh-frontalpole 0 697 4033 wm-rh-temporalpole 0 698 4034 wm-rh-transversetemporal 0 699 4035 wm-rh-insula 0 700 4100 wm-rh-Unknown 0 701 4101 wm-rh-Corpus_callosum 0 702 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 703 4103 wm-rh-G_cingulate-Isthmus 0 704 4104 wm-rh-G_cingulate-Main_part 0 705 4105 wm-rh-G_cuneus 0 706 4106 wm-rh-G_frontal_inf-Opercular_part 0 707 4107 wm-rh-G_frontal_inf-Orbital_part 0 708 4108 wm-rh-G_frontal_inf-Triangular_part 0 709 4109 wm-rh-G_frontal_middle 0 710 4110 wm-rh-G_frontal_superior 0 711 4111 wm-rh-G_frontomarginal 0 712 4112 wm-rh-G_insular_long 0 713 4113 wm-rh-G_insular_short 0 714 4114 wm-rh-G_and_S_occipital_inferior 0 715 4115 wm-rh-G_occipital_middle 0 716 4116 wm-rh-G_occipital_superior 0 717 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 718 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 719 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 720 4120 wm-rh-G_orbital 0 721 4121 wm-rh-G_paracentral 0 722 4122 wm-rh-G_parietal_inferior-Angular_part 0 723 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 724 4124 wm-rh-G_parietal_superior 0 725 4125 wm-rh-G_postcentral 0 726 4126 wm-rh-G_precentral 0 727 4127 wm-rh-G_precuneus 0 728 4128 wm-rh-G_rectus 0 729 4129 wm-rh-G_subcallosal 0 730 4130 wm-rh-G_subcentral 0 731 4131 wm-rh-G_temporal_inferior 0 732 4132 wm-rh-G_temporal_middle 0 733 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 734 4134 wm-rh-G_temp_sup-Lateral_aspect 0 735 4135 wm-rh-G_temp_sup-Planum_polare 0 736 4136 wm-rh-G_temp_sup-Planum_tempolare 0 737 4137 wm-rh-G_and_S_transverse_frontopolar 0 738 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 739 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 740 4140 wm-rh-Lat_Fissure-post_sgt 0 741 4141 wm-rh-Medial_wall 0 742 4142 wm-rh-Pole_occipital 0 743 4143 wm-rh-Pole_temporal 0 744 4144 wm-rh-S_calcarine 0 745 4145 wm-rh-S_central 0 746 4146 wm-rh-S_central_insula 0 747 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 748 4148 wm-rh-S_cingulate-Marginalis_part 0 749 4149 wm-rh-S_circular_insula_anterior 0 750 4150 wm-rh-S_circular_insula_inferior 0 751 4151 wm-rh-S_circular_insula_superior 0 752 4152 wm-rh-S_collateral_transverse_ant 0 753 4153 wm-rh-S_collateral_transverse_post 0 754 4154 wm-rh-S_frontal_inferior 0 755 4155 wm-rh-S_frontal_middle 0 756 4156 wm-rh-S_frontal_superior 0 757 4157 wm-rh-S_frontomarginal 0 758 4158 wm-rh-S_intermedius_primus-Jensen 0 759 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 760 4160 wm-rh-S_occipital_anterior 0 761 4161 wm-rh-S_occipital_middle_and_Lunatus 0 762 4162 wm-rh-S_occipital_superior_and_transversalis 0 763 4163 wm-rh-S_occipito-temporal_lateral 0 764 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 765 4165 wm-rh-S_orbital-H_shapped 0 766 4166 wm-rh-S_orbital_lateral 0 767 4167 wm-rh-S_orbital_medial-Or_olfactory 0 768 4168 wm-rh-S_paracentral 0 769 4169 wm-rh-S_parieto_occipital 0 770 4170 wm-rh-S_pericallosal 0 771 4171 wm-rh-S_postcentral 0 772 4172 wm-rh-S_precentral-Inferior-part 0 773 4173 wm-rh-S_precentral-Superior-part 0 774 4174 wm-rh-S_subcentral_ant 0 775 4175 wm-rh-S_subcentral_post 0 776 4176 wm-rh-S_suborbital 0 777 4177 wm-rh-S_subparietal 0 778 4178 wm-rh-S_supracingulate 0 779 4179 wm-rh-S_temporal_inferior 0 780 4180 wm-rh-S_temporal_superior 0 781 4181 wm-rh-S_temporal_transverse 0 782 5001 Left-UnsegmentedWhiteMatter 0 783 5002 Right-UnsegmentedWhiteMatter 0 784 5050 Left-SLF1_waypoint 0 785 5051 Left-SLF1-Start 0 786 5052 Left-SLF1-End 0 787 5053 Right-SLF1_waypoint 0 788 5054 Right-SLF1-Start 0 789 5055 Right-SLF1-End 0 790 5056 Left-SLF2_waypoint 0 791 5057 Left-SLF2-Start 0 792 5058 Left-SLF2-End 0 793 5059 Right-SLF2_waypoint 0 794 5060 Right-SLF2-Start 0 795 5061 Right-SLF2-End 0 796 5062 Left-SLF3_waypoint 0 797 5063 Left-SLF3-Start 0 798 5064 Left-SLF3-End 0 799 5065 Right-SLF3_waypoint 0 800 5066 Right-SLF3-Start 0 801 5067 Right-SLF3-End 0 802 5068 Left-CST_waypoint 0 803 5069 Left-CST-Start 0 804 5070 Left-CST-End 0 805 5071 Right-CST_waypoint 0 806 5072 Right-CST-Start 0 807 5073 Right-CST-End 0 808 5074 Left-Cingulum_Body_waypoint 0 809 5075 Left-Cingulum_Body-Start 0 810 5076 Left-Cingulum_Body-End 0 811 5077 Right-Cingulum_Body_waypoint 0 812 5078 Right-Cingulum_Body-Start 0 813 5079 Right-Cingulum_Body-End 0 814 5080 Left-Uncinate_Fasciculus_waypoint 0 815 5081 Left-Uncinate_Fasciculus-Start 0 816 5082 Left-Uncinate_Fasciculus-End 0 817 5083 Right-Uncinate_Fasciculus_waypoint 0 818 5084 Right-Uncinate_Fasciculus-Start 0 819 5085 Right-Uncinate_Fasciculus-End 0 820 5086 Left-Inf-Fronto-occ-Fasc_waypoint 0 821 5087 Left-Inf-Fronto-occ-Fasc-Start 0 822 5088 Left-Inf-Fronto-occ-Fasc-End 0 823 5089 Right-Inf-Fronto-occ-Fasc_waypoint 0 824 5090 Right-Inf-Fronto-occ-Fasc-Start 0 825 5091 Right-Inf-Fronto-occ-Fasc-End 0 826 5092 Left-Sup-Fronto-occ-Fasc_waypoint 0 827 5093 Left-Sup-Fronto-occ-Fasc-Start 0 828 5094 Left-Sup-Fronto-occ-Fasc-End 0 829 5095 Right-Sup-Fronto-occ-Fasc_waypoint 0 830 5096 Right-Sup-Fronto-occ-Fasc-Start 0 831 5097 Right-Sup-Fronto-occ-Fasc-End 0 832 5098 Left-Inf-Longitudinal-Fasc_waypoint 0 833 5099 Left-Inf-Longitudinal-Fasc-Start 0 834 5100 Left-Inf-Longitudinal-Fasc-End 0 835 5101 Right-Inf-Longitudinal-Fasc_waypoint 0 836 5102 Right-Inf-Longitudinal-Fasc-Start 0 837 5103 Right-Inf-Longitudinal-Fasc-End 0 838 5104 Right-Occipital-optic-radiation-Start 0 839 5105 Right-Occipital-optic-radiation-waypoint 0 840 5106 Right-Occipital-optic-radiation-End 0 841 5107 Left-Occipital-optic-radiation-Start 0 842 5108 Left-Occipital-optic-radiation-waypoint 0 843 5109 Left-Occipital-optic-radiation-End 0 844 5110 Right-Temporal-optic-radiation-start 0 845 5111 Right-Temporal-optic-radiation-waypoint 0 846 5112 Right-Temporal-optic-radiation-end 0 847 5113 Left-Temporal-optic-radiation-start 0 848 5114 Left-Temporal-optic-radiation-waypoint 0 849 5115 Left-Temporal-optic-radiation-end 0 850 6000 CST-orig 0 851 6001 CST-hammer 0 852 6002 CST-CVS 0 853 6003 CST-flirt 0 854 6010 Left-SLF1 0 855 6020 Right-SLF1 0 856 6030 Left-SLF3 0 857 6040 Right-SLF3 0 858 6050 Left-CST 0 859 6060 Right-CST 0 860 6070 Left-SLF2 0 861 6080 Right-SLF2 0 862 7001 Lateral-nucleus 0 863 7002 Basolateral-nucleus 0 864 7003 Basal-nucleus 0 865 7004 Centromedial-nucleus 0 866 7005 Central-nucleus 0 867 7006 Medial-nucleus 0 868 7007 Cortical-nucleus 0 869 7008 Accessory-Basal-nucleus 0 870 7009 Corticoamygdaloid-transitio 0 871 7010 Anterior-amygdaloid-area-AAA 0 872 7011 Fusion-amygdala-HP-FAH 0 873 7012 Hippocampal-amygdala-transition-HATA 0 874 7013 Endopiriform-nucleus 0 875 7014 Lateral-nucleus-olfactory-tract 0 876 7015 Paralaminar-nucleus 0 877 7016 Intercalated-nucleus 0 878 7017 Prepiriform-cortex 0 879 7018 Periamygdaloid-cortex 0 880 7019 Envelope-Amygdala 0 881 7020 Extranuclear-Amydala 0 882 7100 Brainstem-inferior-colliculus 0 883 7101 Brainstem-cochlear-nucleus 0 884 8001 Thalamus-Anterior 0 885 8002 Thalamus-Ventral-anterior 0 886 8003 Thalamus-Lateral-dorsal 0 887 8004 Thalamus-Lateral-posterior 0 888 8005 Thalamus-Ventral-lateral 0 889 8006 Thalamus-Ventral-posterior-medial 0 890 8007 Thalamus-Ventral-posterior-lateral 0 891 8008 Thalamus-intralaminar 0 892 8009 Thalamus-centromedian 0 893 8010 Thalamus-mediodorsal 0 894 8011 Thalamus-medial 0 895 8012 Thalamus-pulvinar 0 896 8013 Thalamus-lateral-geniculate 0 897 8014 Thalamus-medial-geniculate 0 898 11100 ctx_lh_Unknown 0 899 11101 ctx_lh_G_and_S_frontomargin 0 900 11102 ctx_lh_G_and_S_occipital_inf 0 901 11103 ctx_lh_G_and_S_paracentral 0 902 11104 ctx_lh_G_and_S_subcentral 0 903 11105 ctx_lh_G_and_S_transv_frontopol 0 904 11106 ctx_lh_G_and_S_cingul-Ant 0 905 11107 ctx_lh_G_and_S_cingul-Mid-Ant 0 906 11108 ctx_lh_G_and_S_cingul-Mid-Post 0 907 11109 ctx_lh_G_cingul-Post-dorsal 0 908 11110 ctx_lh_G_cingul-Post-ventral 0 909 11111 ctx_lh_G_cuneus 0 910 11112 ctx_lh_G_front_inf-Opercular 0 911 11113 ctx_lh_G_front_inf-Orbital 0 912 11114 ctx_lh_G_front_inf-Triangul 0 913 11115 ctx_lh_G_front_middle 0 914 11116 ctx_lh_G_front_sup 0 915 11117 ctx_lh_G_Ins_lg_and_S_cent_ins 0 916 11118 ctx_lh_G_insular_short 0 917 11119 ctx_lh_G_occipital_middle 0 918 11120 ctx_lh_G_occipital_sup 0 919 11121 ctx_lh_G_oc-temp_lat-fusifor 0 920 11122 ctx_lh_G_oc-temp_med-Lingual 0 921 11123 ctx_lh_G_oc-temp_med-Parahip 0 922 11124 ctx_lh_G_orbital 0 923 11125 ctx_lh_G_pariet_inf-Angular 0 924 11126 ctx_lh_G_pariet_inf-Supramar 0 925 11127 ctx_lh_G_parietal_sup 0 926 11128 ctx_lh_G_postcentral 0 927 11129 ctx_lh_G_precentral 0 928 11130 ctx_lh_G_precuneus 0 929 11131 ctx_lh_G_rectus 0 930 11132 ctx_lh_G_subcallosal 0 931 11133 ctx_lh_G_temp_sup-G_T_transv 0 932 11134 ctx_lh_G_temp_sup-Lateral 0 933 11135 ctx_lh_G_temp_sup-Plan_polar 0 934 11136 ctx_lh_G_temp_sup-Plan_tempo 0 935 11137 ctx_lh_G_temporal_inf 0 936 11138 ctx_lh_G_temporal_middle 0 937 11139 ctx_lh_Lat_Fis-ant-Horizont 0 938 11140 ctx_lh_Lat_Fis-ant-Vertical 0 939 11141 ctx_lh_Lat_Fis-post 0 940 11142 ctx_lh_Medial_wall 0 941 11143 ctx_lh_Pole_occipital 0 942 11144 ctx_lh_Pole_temporal 0 943 11145 ctx_lh_S_calcarine 0 944 11146 ctx_lh_S_central 0 945 11147 ctx_lh_S_cingul-Marginalis 0 946 11148 ctx_lh_S_circular_insula_ant 0 947 11149 ctx_lh_S_circular_insula_inf 0 948 11150 ctx_lh_S_circular_insula_sup 0 949 11151 ctx_lh_S_collat_transv_ant 0 950 11152 ctx_lh_S_collat_transv_post 0 951 11153 ctx_lh_S_front_inf 0 952 11154 ctx_lh_S_front_middle 0 953 11155 ctx_lh_S_front_sup 0 954 11156 ctx_lh_S_interm_prim-Jensen 0 955 11157 ctx_lh_S_intrapariet_and_P_trans 0 956 11158 ctx_lh_S_oc_middle_and_Lunatus 0 957 11159 ctx_lh_S_oc_sup_and_transversal 0 958 11160 ctx_lh_S_occipital_ant 0 959 11161 ctx_lh_S_oc-temp_lat 0 960 11162 ctx_lh_S_oc-temp_med_and_Lingual 0 961 11163 ctx_lh_S_orbital_lateral 0 962 11164 ctx_lh_S_orbital_med-olfact 0 963 11165 ctx_lh_S_orbital-H_Shaped 0 964 11166 ctx_lh_S_parieto_occipital 0 965 11167 ctx_lh_S_pericallosal 0 966 11168 ctx_lh_S_postcentral 0 967 11169 ctx_lh_S_precentral-inf-part 0 968 11170 ctx_lh_S_precentral-sup-part 0 969 11171 ctx_lh_S_suborbital 0 970 11172 ctx_lh_S_subparietal 0 971 11173 ctx_lh_S_temporal_inf 0 972 11174 ctx_lh_S_temporal_sup 0 973 11175 ctx_lh_S_temporal_transverse 0 974 12100 ctx_rh_Unknown 0 975 12101 ctx_rh_G_and_S_frontomargin 0 976 12102 ctx_rh_G_and_S_occipital_inf 0 977 12103 ctx_rh_G_and_S_paracentral 0 978 12104 ctx_rh_G_and_S_subcentral 0 979 12105 ctx_rh_G_and_S_transv_frontopol 0 980 12106 ctx_rh_G_and_S_cingul-Ant 0 981 12107 ctx_rh_G_and_S_cingul-Mid-Ant 0 982 12108 ctx_rh_G_and_S_cingul-Mid-Post 0 983 12109 ctx_rh_G_cingul-Post-dorsal 0 984 12110 ctx_rh_G_cingul-Post-ventral 0 985 12111 ctx_rh_G_cuneus 0 986 12112 ctx_rh_G_front_inf-Opercular 0 987 12113 ctx_rh_G_front_inf-Orbital 0 988 12114 ctx_rh_G_front_inf-Triangul 0 989 12115 ctx_rh_G_front_middle 0 990 12116 ctx_rh_G_front_sup 0 991 12117 ctx_rh_G_Ins_lg_and_S_cent_ins 0 992 12118 ctx_rh_G_insular_short 0 993 12119 ctx_rh_G_occipital_middle 0 994 12120 ctx_rh_G_occipital_sup 0 995 12121 ctx_rh_G_oc-temp_lat-fusifor 0 996 12122 ctx_rh_G_oc-temp_med-Lingual 0 997 12123 ctx_rh_G_oc-temp_med-Parahip 0 998 12124 ctx_rh_G_orbital 0 999 12125 ctx_rh_G_pariet_inf-Angular 0 1000 12126 ctx_rh_G_pariet_inf-Supramar 0 1001 12127 ctx_rh_G_parietal_sup 0 1002 12128 ctx_rh_G_postcentral 0 1003 12129 ctx_rh_G_precentral 0 1004 12130 ctx_rh_G_precuneus 0 1005 12131 ctx_rh_G_rectus 0 1006 12132 ctx_rh_G_subcallosal 0 1007 12133 ctx_rh_G_temp_sup-G_T_transv 0 1008 12134 ctx_rh_G_temp_sup-Lateral 0 1009 12135 ctx_rh_G_temp_sup-Plan_polar 0 1010 12136 ctx_rh_G_temp_sup-Plan_tempo 0 1011 12137 ctx_rh_G_temporal_inf 0 1012 12138 ctx_rh_G_temporal_middle 0 1013 12139 ctx_rh_Lat_Fis-ant-Horizont 0 1014 12140 ctx_rh_Lat_Fis-ant-Vertical 0 1015 12141 ctx_rh_Lat_Fis-post 0 1016 12142 ctx_rh_Medial_wall 0 1017 12143 ctx_rh_Pole_occipital 0 1018 12144 ctx_rh_Pole_temporal 0 1019 12145 ctx_rh_S_calcarine 0 1020 12146 ctx_rh_S_central 0 1021 12147 ctx_rh_S_cingul-Marginalis 0 1022 12148 ctx_rh_S_circular_insula_ant 0 1023 12149 ctx_rh_S_circular_insula_inf 0 1024 12150 ctx_rh_S_circular_insula_sup 0 1025 12151 ctx_rh_S_collat_transv_ant 0 1026 12152 ctx_rh_S_collat_transv_post 0 1027 12153 ctx_rh_S_front_inf 0 1028 12154 ctx_rh_S_front_middle 0 1029 12155 ctx_rh_S_front_sup 0 1030 12156 ctx_rh_S_interm_prim-Jensen 0 1031 12157 ctx_rh_S_intrapariet_and_P_trans 0 1032 12158 ctx_rh_S_oc_middle_and_Lunatus 0 1033 12159 ctx_rh_S_oc_sup_and_transversal 0 1034 12160 ctx_rh_S_occipital_ant 0 1035 12161 ctx_rh_S_oc-temp_lat 0 1036 12162 ctx_rh_S_oc-temp_med_and_Lingual 0 1037 12163 ctx_rh_S_orbital_lateral 0 1038 12164 ctx_rh_S_orbital_med-olfact 0 1039 12165 ctx_rh_S_orbital-H_Shaped 0 1040 12166 ctx_rh_S_parieto_occipital 0 1041 12167 ctx_rh_S_pericallosal 0 1042 12168 ctx_rh_S_postcentral 0 1043 12169 ctx_rh_S_precentral-inf-part 0 1044 12170 ctx_rh_S_precentral-sup-part 0 1045 12171 ctx_rh_S_suborbital 0 1046 12172 ctx_rh_S_subparietal 0 1047 12173 ctx_rh_S_temporal_inf 0 1048 12174 ctx_rh_S_temporal_sup 0 1049 12175 ctx_rh_S_temporal_transverse 0 1050 13100 wm_lh_Unknown 0 1051 13101 wm_lh_G_and_S_frontomargin 0 1052 13102 wm_lh_G_and_S_occipital_inf 0 1053 13103 wm_lh_G_and_S_paracentral 0 1054 13104 wm_lh_G_and_S_subcentral 0 1055 13105 wm_lh_G_and_S_transv_frontopol 0 1056 13106 wm_lh_G_and_S_cingul-Ant 0 1057 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 1058 13108 wm_lh_G_and_S_cingul-Mid-Post 0 1059 13109 wm_lh_G_cingul-Post-dorsal 0 1060 13110 wm_lh_G_cingul-Post-ventral 0 1061 13111 wm_lh_G_cuneus 0 1062 13112 wm_lh_G_front_inf-Opercular 0 1063 13113 wm_lh_G_front_inf-Orbital 0 1064 13114 wm_lh_G_front_inf-Triangul 0 1065 13115 wm_lh_G_front_middle 0 1066 13116 wm_lh_G_front_sup 0 1067 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 1068 13118 wm_lh_G_insular_short 0 1069 13119 wm_lh_G_occipital_middle 0 1070 13120 wm_lh_G_occipital_sup 0 1071 13121 wm_lh_G_oc-temp_lat-fusifor 0 1072 13122 wm_lh_G_oc-temp_med-Lingual 0 1073 13123 wm_lh_G_oc-temp_med-Parahip 0 1074 13124 wm_lh_G_orbital 0 1075 13125 wm_lh_G_pariet_inf-Angular 0 1076 13126 wm_lh_G_pariet_inf-Supramar 0 1077 13127 wm_lh_G_parietal_sup 0 1078 13128 wm_lh_G_postcentral 0 1079 13129 wm_lh_G_precentral 0 1080 13130 wm_lh_G_precuneus 0 1081 13131 wm_lh_G_rectus 0 1082 13132 wm_lh_G_subcallosal 0 1083 13133 wm_lh_G_temp_sup-G_T_transv 0 1084 13134 wm_lh_G_temp_sup-Lateral 0 1085 13135 wm_lh_G_temp_sup-Plan_polar 0 1086 13136 wm_lh_G_temp_sup-Plan_tempo 0 1087 13137 wm_lh_G_temporal_inf 0 1088 13138 wm_lh_G_temporal_middle 0 1089 13139 wm_lh_Lat_Fis-ant-Horizont 0 1090 13140 wm_lh_Lat_Fis-ant-Vertical 0 1091 13141 wm_lh_Lat_Fis-post 0 1092 13142 wm_lh_Medial_wall 0 1093 13143 wm_lh_Pole_occipital 0 1094 13144 wm_lh_Pole_temporal 0 1095 13145 wm_lh_S_calcarine 0 1096 13146 wm_lh_S_central 0 1097 13147 wm_lh_S_cingul-Marginalis 0 1098 13148 wm_lh_S_circular_insula_ant 0 1099 13149 wm_lh_S_circular_insula_inf 0 1100 13150 wm_lh_S_circular_insula_sup 0 1101 13151 wm_lh_S_collat_transv_ant 0 1102 13152 wm_lh_S_collat_transv_post 0 1103 13153 wm_lh_S_front_inf 0 1104 13154 wm_lh_S_front_middle 0 1105 13155 wm_lh_S_front_sup 0 1106 13156 wm_lh_S_interm_prim-Jensen 0 1107 13157 wm_lh_S_intrapariet_and_P_trans 0 1108 13158 wm_lh_S_oc_middle_and_Lunatus 0 1109 13159 wm_lh_S_oc_sup_and_transversal 0 1110 13160 wm_lh_S_occipital_ant 0 1111 13161 wm_lh_S_oc-temp_lat 0 1112 13162 wm_lh_S_oc-temp_med_and_Lingual 0 1113 13163 wm_lh_S_orbital_lateral 0 1114 13164 wm_lh_S_orbital_med-olfact 0 1115 13165 wm_lh_S_orbital-H_Shaped 0 1116 13166 wm_lh_S_parieto_occipital 0 1117 13167 wm_lh_S_pericallosal 0 1118 13168 wm_lh_S_postcentral 0 1119 13169 wm_lh_S_precentral-inf-part 0 1120 13170 wm_lh_S_precentral-sup-part 0 1121 13171 wm_lh_S_suborbital 0 1122 13172 wm_lh_S_subparietal 0 1123 13173 wm_lh_S_temporal_inf 0 1124 13174 wm_lh_S_temporal_sup 0 1125 13175 wm_lh_S_temporal_transverse 0 1126 14100 wm_rh_Unknown 0 1127 14101 wm_rh_G_and_S_frontomargin 0 1128 14102 wm_rh_G_and_S_occipital_inf 0 1129 14103 wm_rh_G_and_S_paracentral 0 1130 14104 wm_rh_G_and_S_subcentral 0 1131 14105 wm_rh_G_and_S_transv_frontopol 0 1132 14106 wm_rh_G_and_S_cingul-Ant 0 1133 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 1134 14108 wm_rh_G_and_S_cingul-Mid-Post 0 1135 14109 wm_rh_G_cingul-Post-dorsal 0 1136 14110 wm_rh_G_cingul-Post-ventral 0 1137 14111 wm_rh_G_cuneus 0 1138 14112 wm_rh_G_front_inf-Opercular 0 1139 14113 wm_rh_G_front_inf-Orbital 0 1140 14114 wm_rh_G_front_inf-Triangul 0 1141 14115 wm_rh_G_front_middle 0 1142 14116 wm_rh_G_front_sup 0 1143 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 1144 14118 wm_rh_G_insular_short 0 1145 14119 wm_rh_G_occipital_middle 0 1146 14120 wm_rh_G_occipital_sup 0 1147 14121 wm_rh_G_oc-temp_lat-fusifor 0 1148 14122 wm_rh_G_oc-temp_med-Lingual 0 1149 14123 wm_rh_G_oc-temp_med-Parahip 0 1150 14124 wm_rh_G_orbital 0 1151 14125 wm_rh_G_pariet_inf-Angular 0 1152 14126 wm_rh_G_pariet_inf-Supramar 0 1153 14127 wm_rh_G_parietal_sup 0 1154 14128 wm_rh_G_postcentral 0 1155 14129 wm_rh_G_precentral 0 1156 14130 wm_rh_G_precuneus 0 1157 14131 wm_rh_G_rectus 0 1158 14132 wm_rh_G_subcallosal 0 1159 14133 wm_rh_G_temp_sup-G_T_transv 0 1160 14134 wm_rh_G_temp_sup-Lateral 0 1161 14135 wm_rh_G_temp_sup-Plan_polar 0 1162 14136 wm_rh_G_temp_sup-Plan_tempo 0 1163 14137 wm_rh_G_temporal_inf 0 1164 14138 wm_rh_G_temporal_middle 0 1165 14139 wm_rh_Lat_Fis-ant-Horizont 0 1166 14140 wm_rh_Lat_Fis-ant-Vertical 0 1167 14141 wm_rh_Lat_Fis-post 0 1168 14142 wm_rh_Medial_wall 0 1169 14143 wm_rh_Pole_occipital 0 1170 14144 wm_rh_Pole_temporal 0 1171 14145 wm_rh_S_calcarine 0 1172 14146 wm_rh_S_central 0 1173 14147 wm_rh_S_cingul-Marginalis 0 1174 14148 wm_rh_S_circular_insula_ant 0 1175 14149 wm_rh_S_circular_insula_inf 0 1176 14150 wm_rh_S_circular_insula_sup 0 1177 14151 wm_rh_S_collat_transv_ant 0 1178 14152 wm_rh_S_collat_transv_post 0 1179 14153 wm_rh_S_front_inf 0 1180 14154 wm_rh_S_front_middle 0 1181 14155 wm_rh_S_front_sup 0 1182 14156 wm_rh_S_interm_prim-Jensen 0 1183 14157 wm_rh_S_intrapariet_and_P_trans 0 1184 14158 wm_rh_S_oc_middle_and_Lunatus 0 1185 14159 wm_rh_S_oc_sup_and_transversal 0 1186 14160 wm_rh_S_occipital_ant 0 1187 14161 wm_rh_S_oc-temp_lat 0 1188 14162 wm_rh_S_oc-temp_med_and_Lingual 0 1189 14163 wm_rh_S_orbital_lateral 0 1190 14164 wm_rh_S_orbital_med-olfact 0 1191 14165 wm_rh_S_orbital-H_Shaped 0 1192 14166 wm_rh_S_parieto_occipital 0 1193 14167 wm_rh_S_pericallosal 0 1194 14168 wm_rh_S_postcentral 0 1195 14169 wm_rh_S_precentral-inf-part 0 1196 14170 wm_rh_S_precentral-sup-part 0 1197 14171 wm_rh_S_suborbital 0 1198 14172 wm_rh_S_subparietal 0 1199 14173 wm_rh_S_temporal_inf 0 1200 14174 wm_rh_S_temporal_sup 0 1201 14175 wm_rh_S_temporal_transverse 0

2 1

high-resolution cerebellar surface map
by Judy Kipping 18 Apr '11

18 Apr '11

Dear freesurfer community, I have started using freesurfer in order to visualize functional data of the cerebellum on a surface map. I was reading a lot in the freesurfer archives, and have found entries discussing or asking about a progress in order to properly segment and map highly resolved anatomical data (in my case 0.5x0.5x0.6). After some time now I managed to create surface maps, going stepwise through the recon-all scripts to improve cerebellar segmentation. But still, I struggle with parameter settings in autorecon-2. Do you have any suggestions on parameters which might have a crucial benefit in order to keep the folia of cerebellar cortex maintained? However, I was also wondering, whether the experts can report something new at the 'automatic cerebellar segmentation' front. I highly appreciate any advice! Thanks, Judy Kipping

1 0

High resolution segmentation
by Jahfari, Sara 18 Apr '11

18 Apr '11

Dear Freesurfer crew, We would like to use freesurfer to do the high resolution parcellation of gray matter reported in Hagmann et all. 2008. This far I have used (looking also at previous postings on this matter) mris_divide_parcellation pp0672 rh aparc.annot 150 rh.split150.annot (but this creates a parcellation of long strips per region, that is not fully suited for what we want). mris_make_face_parcellation lh.inflated $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot The make_face_parcellation looks very nice, but I have the following questions: 1. How can I convert the .annot file to an actual .mgz volume segmentation. ( I have tried mri_annotation2label but I am not sure how the — segbase should be specified) 2. Is there a way to match the aparc.annot labels to the ic3.annot parcellation (in the way that is done with mris_divide_parcellation) ( I have converted the both annot files to labels to look at the vertex numbers, but preferably I would like the eventual segmentation to contain label info’s per volume such as in aparc+aseg.mgz) Any help would be appreciated a lot. Thanks, Sara

2 1

install tracula
by John Fredy 18 Apr '11

18 Apr '11

Hello all I am doing the tutorial about tracula ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula) but I can`t find the trac-all command in my system. I was running freesurfer 4.5, and now I am running freesurfer 5, but I can´t see the executable in any folder Thanks in advance John Ochoa

2 2

Convert transforms from xfm to lta
by Matt Glasser 17 Apr '11

17 Apr '11

Is it possible to convert an .xfm to an .lta or alternatively to initialize mri_em_register with an .xfm that one has manually generated? It is not doing a very good job for me. Thanks, Matt.

2 1

Non-linear Volumetric Registration
by Tetiana Dadakova 17 Apr '11

17 Apr '11

Dear list, Could you please recommend me the literature on non-linear volumetric registration used in FS? Also, is there a possibility to view talairach.m3z file? Thank you, Tanja.

2 1

Re: [Freesurfer] install tracula
by Allison Stevens 15 Apr '11

15 Apr '11

Sorry, I meant not in 5.0. > > On Fri, Apr 15, 2011 at 19:29, Allison Stevens > <astevens(a)nmr.mgh.harvard.edu> wrote: >> John, >> Tracula is available in the soon to be released 5.1 but not in 5.1. >> Allison >> >> On Fri, 15 Apr 2011, John Fredy wrote: >> >>> Hello all >>> >>> I am doing the tutorial about tracula ( >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula) but I can`t >>> find the trac-all command in my system. I was running freesurfer 4.5, and >>> now I am running >>> freesurfer 5, but I can´t see the executable in any folder >>> >>> Thanks in advance >>> >>> John Ochoa >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > >

1 0

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