External Email - Use Caution Hi Doug,
I think I may have found a similar issue via the mailing list which I hadn't noticed before. However, it's not clear to me how to implement this solution. https://secure-web.cisco.com/1uK1SqmLnsjHZpvlRJyITHKYUhsrOBcU7gkc7GagN0OUsbxgbuaXR7mJEmN0D9LHVvpNjZScCPthfFK0-9DMt-JMGIobJ0Nwvjv6_dhtQwajnyRV-kWYGhspgxGFAHobEFgm1BMAz6KLv1bPDs0bfsrNkxyEXnOh89JZKO57Zx_8Y28sU2xHewG4MD2qUokz-rsz_Q-LS4Sm1TweiFTdAd5rdvZ1_CIQ58pI-qz5T-dSCp-XWl7LVsG22IpD_nFN8juENy27iFWfgh-2IhA3NYK7kXMdWYfu_s5zrX-0_JlLlPfDnE6F53WSFLralPOyd/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg56796.html Any ideas? On Tue, Jun 21, 2022 at 1:48 PM Benjamin Deck <bdeck8...@gmail.com> wrote: > Hi Doug, > > Thanks for getting back to me. > > Yes, it's very weird. My LUT doesn't contain any subcortical structures > but when I load my custom LUT into Freeview, it shows my surface-based > parcellation in the subcortical regions. Furthermore, my annotation files > look completely fine! > > I noticed that the indices of my LUT are the same as the default LUT, > could this be a problem; should my custom LUT have unique index IDs? > > For example see the two LUTs: > > > *FS default LUT:* > #No. Label Name: R G B A > > 0 Unknown 0 0 0 0 > 1 Left-Cerebral-Exterior 70 130 180 0 > 2 Left-Cerebral-White-Matter 245 245 245 0 > 3 Left-Cerebral-Cortex 205 62 78 0 > 4 Left-Lateral-Ventricle 120 18 134 0 > 5 Left-Inf-Lat-Vent 196 58 250 0 > 6 Left-Cerebellum-Exterior 0 148 0 0 > 7 Left-Cerebellum-White-Matter 220 248 164 0 > ..... > > *My Custom LUT* > 0 Unknown 0 0 0 0 > 1 Net_10_ROIs_1_lh_native 255 255 255 0 > 2 Net_11_ROIs_1_lh_native 25 5 25 0 > 3 Net_12_ROIs_1_lh_native 25 100 40 0 > 4 Net_12_ROIs_2_lh_native 70 130 180 0 > 5 Net_13_ROIs_1_lh_native 100 100 0 0 > 6 Net_13_ROIs_2_lh_native 196 58 250 0 > 7 Net_13_ROIs_3_lh_native 100 25 0 0 > ..... > > *Output from the call with your suggestion of --aseg flag:* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table > sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask --aseg > aseg.presurf.hyposSUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjectssubject > sub-DAEKoutvol > /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgzuseribbon > 0baseoffset 0RipUnknown 18 avail.processors, using 6Reading lh white > surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.whiteReading > lh pial > surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.pialLoading > lh annotations from > /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annotHave > color table for lh white annotationRipping vertices labeled as unkownRipped > 27062 vertices from left hemiBuilding hash of lh whiteBuilding hash of lh > pialReading rh white > surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.whiteReading > rh pial > surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.pialLoading > rh annotations from > /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annotHave > color table for rh white annotationRipping vertices labeled as unkownRipped > 27560 vertices from right hemiBuilding hash of rh whiteBuilding hash of rh > pialLoading ribbon segmentation from > /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgzLoading aseg > from > /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/aseg.presurf.hypos.mgzASeg > Vox2RAS: ------------0.80000 0.00000 0.00000 127.99999; 0.00000 > 0.00000 0.80000 -127.99999; 0.00000 -0.80000 0.00000 > 127.99999; 0.00000 0.00000 0.00000 > 1.00000;-------------------------Labeling Slice (320)161 108 214 54 0 > 267 1 55 268 2 269 56 3 270 57 4 271 58 272 5 59 6 273 60 > 7 274 61 275 8 62 276 9 63 277 10 64 278 11 65 279 12 66 280 > 67 13 281 68 14 282 15 69 283 16 284 70 17 285 18 286 19287 20 > 71 288 21 289 22 290 23 291 24 292 25 293 26 294 27 295 28 72 296 > 29 297 30 298 31 299 32 300 33 301 34 302 35 303 36 304 37 38 305 > 39306 40 307 41 308 42 309 43 310 44 311 45 73 312 46 313 47 314 > 48 315 49 316 50 317 51 318 52 319 53 74 75 76 77 78 79109 162 > 80 215 81 82 163 110 83 216 164 84 111 85 165 86 217 112 87 166 88 > 218 113 89 167 90 219114 91 168 115 92 220 169 93 116 221 94 117 170 > 222 95 118 96 223 171 119 97 224 172 120 225 98 226 121 99173 227 100 > 122 228 174 101 123 229 102 230 175 124 103 231 176 232 125 104 233 234 105 > 177 126 235 236 106 178 127 237 238 107 239179240 128 241 242 243 180 244 > 129 245 246 247 248 181 249 250 251 130 252 253 254 255 256 257 258 259260 > 261 262 263 264 265 266 182 183 131 184 185 186 132 187 188 133 189 190 134 > 191 135 192 193 136 194 137 195 138 196 139197 140 198 141 199142 200 201 > 143 202 144 203 145 204 205 146 206 147 207 148 208 149 209 150 210 151 211 > 152 212 153 213 154 155 156 157 158 159160 nctx = 1191735Used brute-force > search on 1567 voxelsWriting output aseg to > /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgz#VMPC# > mri_aparc2aseg VmPeak 2534656mri_aparc2aseg done* > > > <https://secure-web.cisco.com/1OO2IC4GJ9uoy1IqNmDJgrYeKv1GnylWJbOS45mHkjS0Xoil32F2xBG3i2QeWolF-kYM-nxJM8avUB2h8G39NyR_fP-M_hd3HXjvm9IfzciZ-FIWL4DRHgiRzxfqzI1ko5z0mT92eLKfMTyJhL8_NIWeHLx5T8-FKXbG07m5E-ZLJeZwL_JNMCi8dyD14FII3Uo21lmcQwLHppym7Eu6y-Hrwr8ku_G9ci1989uzgjfgA_f-x3ylQl7jvC8vgc9mWab3kBCU9izcZxORqNpi1nUBbUaRqgiAXluEKwfIlQLHwTJDEJaAQ5J1wP5-4EpQt/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon> > Virus-free. > http://secure-web.cisco.com/1a0bIqutTEiBBbR1_nuFcj6dIklLFvjcL6F9ORFBYYmhEun_sa_OR5iPqicIGV1HLhkPApWedF-avmXYpDMbvOKWSCw7__rHIWlNWTHmWLH07YjV14Ypo1YLEKq-JR7YwJgHNfD2x4v-rFmoE75ilKcnApzBVhr9kF2Fgc8W4EVu06qDf3ufYyHLbyb1cPEuuaLHXLu1zLhTmIDTStIOR3PpoxnbhlfmZkOgEU4tF1zs-6rPAJ1CIjX1bZ5tp7T6eI2ysO9zRscsGfwVwONbm6pKKf8PvwZiOe67EfiUe_z4XJLWEyKho8ft0ZHUB4CMO/http%3A%2F%2Fwww.avast.com > <https://secure-web.cisco.com/1v3dk3IfkCt00BOR8Qf-wWFtThne2Ut2kN2k-zpIBZbBWfAWRq25RQW99zoxuwKtRX5cD2J5MllJkl051rDzMd-CMl9D_eOkbQem2xM42r9bmneJyvyZF3CU8x5iDWdgccn00OPod0Y-EIXnpu-2mp0-XLPMerbJj4-uqRtg1uIb1qsPL-y_kuW7qFKkzBgj-Mm7nbAFQyqOdPuPTCZ5zk3NdGg6U_7BKzl9VjJno2xWM4iCMZkl1Qq2Hl7UxMsrftIzYfaLYPYFijNVMbDrzijSGQwyXwcSuMNZL3M3WA_WZPMtPKEgqVxhXu0H8YyXF/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink> > <#m_2217728403180872500_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > On Sun, Jun 19, 2022 at 10:47 AM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> I'm not sure what is happening. Does cortex have label value that are >> just not in the LUT or are the values 0? >> Try adding --aseg aseg.presurf.hypos >> If you need more help,make sure to include the full terminal output >> >> On 6/13/2022 4:49 PM, Benjamin Deck wrote: >> >> External Email - Use Caution >> Hi Freesurfer experts, >> >> I am attempting to turn my surface-based parcellation into a segmentation >> file using the following command: >> >> mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table >> sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask >> >> However, when I load the resulting volume using my custom LUT the ROIs >> get labeled to the white matter and subcortical structures leaving the grey >> matter unlabeled. >> >> When I examine the annotation files, they look appropriate and there >> isn't any overlap. >> >> Do I need to include the subcortical structures in my custom LUT to avoid >> this from happening or is there a better solution? >> >> Thank you! >> >> -- >> *Benjamin L. Deck* >> *Doctoral Student* >> *Applied Cognitive and Brain Sciences* >> *Department of Psychological and Brain Sciences* >> *Drexel University* >> >> >> <https://secure-web.cisco.com/1QkkGrc1M5CNJQjlaL6JN2C_Kh4FZGHEk5bXUEdRCEnkZGofuM17FsjaC0cgNKVyiw9zseRKNgWl7UYi7kfAZRu5vUOPJlx0s2Ia-QgtX4o_szO3739D63ABkoOt98WW7To36kJ3RGyELj3CK0t-mr__ZFDRKlYyMgt8G25IoLpVvK-TSMOqcxCmaAk6WwPqtiw0bMS6sq328dr7OygGFi5SbdSbNdRmWeipEl9x83zjjTbV0ZbWQl_nq3CIoMq7fqQJZGM0ljgbRsibrJ1UQasx4uStqpHunakdmw0kRTNM6MTMvKIkahwk208sAqQ7V/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon> >> Virus-free. >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> http://secure-web.cisco.com/1a0bIqutTEiBBbR1_nuFcj6dIklLFvjcL6F9ORFBYYmhEun_sa_OR5iPqicIGV1HLhkPApWedF-avmXYpDMbvOKWSCw7__rHIWlNWTHmWLH07YjV14Ypo1YLEKq-JR7YwJgHNfD2x4v-rFmoE75ilKcnApzBVhr9kF2Fgc8W4EVu06qDf3ufYyHLbyb1cPEuuaLHXLu1zLhTmIDTStIOR3PpoxnbhlfmZkOgEU4tF1zs-6rPAJ1CIjX1bZ5tp7T6eI2ysO9zRscsGfwVwONbm6pKKf8PvwZiOe67EfiUe_z4XJLWEyKho8ft0ZHUB4CMO/http%3A%2F%2Fwww.avast.com >> <https://secure-web.cisco.com/1tDhPrZdlS9NSF2Pe-eEm0Zojd9ScbaKYJdMT0872rwJGrh_9EMJhKwa8kdFnfCqEKffeIreGIGq7zK66tIGH7uPQhNpJFxQYtMTzxMVO5dFH9_TICZD8qopdSFWucXDIvtzKANR0O2i1FQikRSjOQ_GGN6VTxcsO3kkgX36vsLpbkHwV7FVeKf2C-6ipxbYlIyKw3xxeYAReIaUptDTHthY7JhObP6a90JAfTWm_nTGkx2g8op8mdJ3wWzUrk12fDdzuMDbAq19is2D55CEHvyNJH96fW0zJ2WaJqmqgKc-o9lwCHUZWPaDKAfswoRRo/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1C7GAoUy5XgfQHJs_ybk3ewCK03OLany2CXNf1Tg39T224mI664Ae3O2CJgcNugDTJHslOOoKbLPo2mUED4qeYjSVzH8DVUnRlAkXhCb0JGf4p5wtMB6bSiunAKm1_5FYm0grvUJQWkgT-w6oJm8jNcRGr0EDcMW_bDxP-5Smm0Y8UE281qwTFhhmHRMeun29XbqA6JVn3kEABA11iax_PS4ADPsVrpnWtXHp6ik5GKahM50qZYiCjo4qfy_EBom7q_yIPlTCxOLYNb1AKK7N8J2Ecmye2bTPFQEEgzUl_lDt8aTUz0WGJtFdodYmmD-y/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> 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 Mass General >> Brigham Compliance HelpLine at >> https://secure-web.cisco.com/1-ZR-zlt2d6LVNayaWp_2rq4hC1wkHy5aM3zklylIII1ZDw2d8IHZHIzs4qFln6K0-WNqYciByJ5uxmvPV2vk6TlXVYEkgAwgcW12pw1oW5ZXqfozb4T_bka_NyghmeB1KPFX5rYKDxORexoHofUtC505YReBcaAML7F7mnR4ZUqYnQZoIT-oNheUri_-UFseYSWavzLFMgmv6qtd7EQ5apGh4k8XnNwDQ6hb40mdhQlxkC1zqChKyVh6TwcnjR-0j_qvBoD770H_XqmlXbY-cK1mOAhueLR5HCMFa20uCNjVMHAfQXRmqpZ-TRO-pnxZ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> < >> https://secure-web.cisco.com/1-ZR-zlt2d6LVNayaWp_2rq4hC1wkHy5aM3zklylIII1ZDw2d8IHZHIzs4qFln6K0-WNqYciByJ5uxmvPV2vk6TlXVYEkgAwgcW12pw1oW5ZXqfozb4T_bka_NyghmeB1KPFX5rYKDxORexoHofUtC505YReBcaAML7F7mnR4ZUqYnQZoIT-oNheUri_-UFseYSWavzLFMgmv6qtd7EQ5apGh4k8XnNwDQ6hb40mdhQlxkC1zqChKyVh6TwcnjR-0j_qvBoD770H_XqmlXbY-cK1mOAhueLR5HCMFa20uCNjVMHAfQXRmqpZ-TRO-pnxZ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >> . >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> > > > -- > *Benjamin L. Deck* > *Doctoral Student* > *Applied Cognitive and Brain Sciences* > *Department of Psychological and Brain Sciences* > *Drexel University* > -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University*
_______________________________________________ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
