External Email - Use Caution Hi Yujing,
Thanks for taking a look. What do you mean by mismatch? The LUT was used to make the annot file. What would generate this mismatch? Here is the output from my mris_label2annot call: mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label 7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317 subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot Thanks, Ben <https://secure-web.cisco.com/1zRfRnNJbztJhB7UFpY-K9ElZkCsAXpOnfc4n5fGn_R5Lv3vYBe-DsvV2hD4RDdJESnYGiwa-L8Usq00gA3vDfDULMiYvXWIzao4-CCFex8VxZnEHyoZHi_w7aOP9zR8Lrr1Y8z3LBtoV6HZW8rn-UKIJUQ6msWLaxB8mg03Gc0PhRJMTE8Qm9XVocf2vYyAJFjmc7lVmM7DazR_v-LV7kBKizsgmbvfoTdGY6GFqZf1ShyhFoJHgc9JeGE4CSemo1hSyhVqXv_Bw__nW7cCDxnOY2v4wavzxDh0mLF-AWtZPFzdq3Yqf7U-O-QMGJJP2/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/1gAt7l98Kbrrw1JExQNkOHE93wFjZTYGIYGqO5FcQuB3NwuZGR6SUGyXzsTyodroRZu2QKg7NI1FoOtVxTcfc_YAIn-qfbOy-dy1vf0EtM-Yp9P9Vf-BxNp-HXRYpBIOnQnBxlrvLjvXLFhzHe4Xvg3JwiMsHHHqWPMZjmHJVEqwyDd7Y3V1pa4v5oU-oaOcoGljLNDGOXV0tI0LlOYTY7gIKAvoZh-2tVy6aeqJtTRfKSXyYMDDI8YxvdRs0rppH0v137Cj4ZUv1ARsQoobZ5a5YVBnZa1xVkizNNRB5JFOo3MeqjDLq9qGFRn_wzMxa/http%3A%2F%2Fwww.avast.com <https://secure-web.cisco.com/1f-mu2Bhnd8i3u9-0Rrkb9wcQs3dpO6ZBXI3wMPsujw2ZJK7q1QiklKYc5v4PhKLfQ0z4dDi4l2bvV044-uH_3p1QKpj0FuhVHGMGmNqlk5yFHVP8S0B1kLbNAyfebWz_FxsbqzvVHe_Eru_OI49E4lYddCw6L56VTcN-ZLd2GctbSCGAo6IcTE3J4e435EfVAK9-Ej29Ps0QkdiQeAWKUJGG4pq_8g32ctjKz8yOQCIAHpTNyeN1F8nvA5ERYFLzYxK4wxHp9_r8CbXNJA0Brqw7JQkXt9yeMv4ypyYq30ft5Wd32XC5GCHOLcYmb4vq/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > Hi Ben, > > > > I was able to reproduce the core dump. In my case, it was because a > mismatch of color scheme between input annotation file and the color table > loaded with the surface. > > > > I suspect it might be the same issue for you too. But I’m not sure what > the right action is to work around this. > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck > *Sent:* Friday, June 10, 2022 11:47 AM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] mri_label2vol fill-ribbon segmentation fault > > > > * External Email - Use Caution * > > Hi there, > > > > Having issues with the following command: > > > > mri_label2vol --annot lh.yeo_2011.annot --temp > /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh > --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz > > > > > > produces the following error: > > > > Number of labels: 0 > Annot File: lh.yeo_2011.annot > Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz > Outut Volume: lh.sub-DAEK_annot_nat.nii.gz > Registration File: (null) > Fill Threshold: 0 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: sub-DAEK > Hemi: lh > UseNewASeg2Vol: 0 > DoLabelStatVol 0 > LabelCodeOffset 0 > setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects > 7.2.0 > Template RAS-to-Vox: -------- > -1.25000 -0.00000 -0.00000 160.00000; > -0.00000 -0.00000 -1.25000 160.00000; > -0.00000 1.25000 -0.00000 160.00000; > -0.00000 -0.00000 -0.00000 1.00000; > Template Voxel Volume: 0.512 > nHits Thresh: 0 > Using Identity Matrix > RegMat: -------- > 1.00000 0.00000 0.00000 0.00000; > 0.00000 1.00000 0.00000 0.00000; > 0.00000 0.00000 1.00000 0.00000; > 0.00000 0.00000 0.00000 1.00000; > Label RAS-to-Vox: -------- > -1.25000 0.00000 0.00000 160.00000; > 0.00000 0.00000 -1.25000 160.00000; > 0.00000 1.25000 0.00000 160.00000; > 0.00000 0.00000 0.00000 1.00000; > INFO: loading surface > /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white > nvertices = 253237 > Reading thickness > /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness > Loading annotations from lh.yeo_2011.annot > annotidmax = 48 > nlabels = 48 > Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz > Mapping > Segmentation fault > > > > > > But when I run the same command without fill-ribbon the process runs to > completion. > > > > Not sure if this is a memory issue or something else. > > > > Ben > > > -- > > *Benjamin L. Deck* > > *Doctoral Student* > > *Applied Cognitive and Brain Sciences* > > *Department of Psychological and Brain Sciences* > > *Drexel University* > > > > [image: Image removed by sender.] > <https://secure-web.cisco.com/1iKwJbETCAUSlHWE3gbz9IWJ4YvkeL0JhP2fGTP_IRLe0YAuJSsGlpOrQHNVfjuiKYqhmSgH5KSYV_gD6T-ANkaBo1hZWN5AQcHGQwryr0EDsu8NqPcxBZV72UfiPAjYeGdUOFXa8ZAiJxtxf0Q72lp00VpPQNLMHYmAkpu-T-1lhDuMYW579S_wn2oo0a0NYH3gCT_0nvVAgRq9VgIDidx0P2oUyENgIAM6sjaEuUnHLfBrU9x9ZKZbmgbb7zcIjaVn8naws7kOTAcRCm7m_HwRuicAaOxXjHM2dP8MTOhvy94l9zWgewN3dP4a3gLUE/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/1gAt7l98Kbrrw1JExQNkOHE93wFjZTYGIYGqO5FcQuB3NwuZGR6SUGyXzsTyodroRZu2QKg7NI1FoOtVxTcfc_YAIn-qfbOy-dy1vf0EtM-Yp9P9Vf-BxNp-HXRYpBIOnQnBxlrvLjvXLFhzHe4Xvg3JwiMsHHHqWPMZjmHJVEqwyDd7Y3V1pa4v5oU-oaOcoGljLNDGOXV0tI0LlOYTY7gIKAvoZh-2tVy6aeqJtTRfKSXyYMDDI8YxvdRs0rppH0v137Cj4ZUv1ARsQoobZ5a5YVBnZa1xVkizNNRB5JFOo3MeqjDLq9qGFRn_wzMxa/http%3A%2F%2Fwww.avast.com > <https://secure-web.cisco.com/1lKwnHJD_3HKNZFq3yBeIxnL1wagOdiYUAdM7xFJLwCTPpWOVxKWfJ_INP6ff3NFDguVU8luyEeB0A_eghbJamJYyDSqV_tvIuNd4MOeGl-FJ1e1Q9h2qfNbONRZmDV88ErPsp3n0dMRCaqJsc3f5gC-yphrEBAq-GC_SI3CxBaBk5RpBMVLxReS5GbzJElOPa8nn81TTTMegPgBS-Gz8Vdq8vzeEoOgzzgWLqaKINJJtoe8TxBUfvIeTXwxCpEoDmkosL38-remOhJy78-FIS0GfZhAAeMG0rVHnSjxyKafzJNYA-z85paoXHDhg-OyE/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 list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1FUT55eeYf35M-JkMc7UcSX6tQwoolQhFqBp-8LICAUTK0wswJKgW_N0VLBuD8TraBJXxv3A6xEtjOi3zHO6u6hS8qtjCvZLT8blEvNFm05eSJH6b8e3aKqHBqbtFAVOULtn9jgTodt8mPW8m3GmSRUmYpxpu9C3Fkzsso7QpJnn8ogCvZ1glcbo1qzY7f0tbdno7w-kyEgSnfbCNbMMoMyfrKVBy_uY9PmTLYP1fcwc9XbQsn81kFW3GvhlFpwBGRN3Le_la1zqvtr5WRJXwA7glAv3TYsHu2WOT_uygJjXNbYUcMNoxCuIb_tjOc9SD/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. 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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*
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