Hi Ben, Just wanted to update you on mris_label2annot command line options.
If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified. Yujing From: Huang, Yujing Sent: Thursday, June 16, 2022 1:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault Hi Ben, I’m learning it myself too. I played it a little more. I see the mismatch can happen if you skip a number in you LUT. Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault 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 [Image removed by sender.]<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. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.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> On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <yhuan...@mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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 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. 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