How does your LUT look like? What is your first line?
For left hemi, your loaded 50 label files to mris_label2annot, but mri_label2vol only reported 48 labels. It looks like you have duplicated RGB in your LUT. I have identified some. See highlighted in red. The duplicated RGB entries can cause problems.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Wednesday, June 22, 2022 2:24 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
External Email - Use Caution Hi Yujing,
Sure thing.
Commands:
mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt
Output: 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 --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt 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 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 16777215 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
command: mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt
output: 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 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label
7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317
subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 8312 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot
---Annotations look fine.
Command: mri_label2vol --o lh.yeo2011_in_nat.mgz --annot ../lh.yeo2011.annot --identity --fill-ribbon --subject sub-DAEK --h emi lh
Output: Number of labels: 0 Annot File: ../lh.yeo2011.annot Template Volume: (null) Outut Volume: lh.yeo2011_in_nat.mgz 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 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.yeo2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault
----Same thing occurs for the right hemi
On Wed, Jun 22, 2022 at 11:42 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,
Do you mean the issue that ‘mri_label2vol –fill-ribbon’ crashes? Can you re-run and provide your mris_label2annot and mri_label2vol command line and output?
I’m not sure I will be able to offer work around, but I would like to understand the problem better for future development.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
External Email - Use Caution Hi Yujing,
It seems that this did not solve the issue. Are there any other reasons why this would occur?
Ben
On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck <bdeck8317@gmail.commailto:bdeck8317@gmail.com> wrote: Hi Yujing,
Thank you. I will give it a try! Can documentation be updated?
Ben
[Image removed by sender.]https://secure-web.cisco.com/1CbfxkRGloea4lW2PK478ps9kqnPQiVPiaHMcsD6pnKbPkj_NH1SmVOBOGFDKKPUorKYgfC5qkC_p6LV8AFgUuBb0iAZtOiQkRV4eWc8fjOJiIskZtyGr2DoUb2VTUVyD44esBqpBAOVtbKEkjyhAWPRYookez7RQorpkco895Bn0oLCIhAR9GMINczuWsXNqDvM9YMkv_Ed8JLqBa0qMN6I2T6nRKkKAkq3GSGk6XTUeT0cKoEUp3OGr7rsEQ_-EkqyR92yFtkdFHemStKToaXILJAliBpi46_Tspmq_Yr80fDe684fjbvr-O3WXEAww/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.comhttps://secure-web.cisco.com/1tOZ5nSv06qa69857jrCclTd3YENq-4Gk0R8zTlVZo__kYkxRrdsEohQaleNqig9ySPT09bAtTCifKMf_OwGSTmpZBCPs8i_BM-j6n9OGztiXhaL3NbOU-7rrucIhcyhnA6BGcjTkpg5xg1A9DpzGjcLBaE-sFwlFOicNzIAxs9EwU_FxBtUr0EtPt-ZNnKnSQ41HR59oshUwNWw25ic3M58ch6CIly9Eyyb-rGH4aYxdYsDff9evt04MgfZh67XWnw5tcDW93z9PRPVOggrV7IdO2cs57eHdU6rbOYkauy7krQJMspzouJ7M9wYnCAjd/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 Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: 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.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.comhttps://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 <YHUANG43@mgh.harvard.edumailto:YHUANG43@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.avast.comhttps://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.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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. 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1KFYgeucywv-sgvlszrUVmMExT1D1wTosDU5A-ke32OnzTiJE16BPNnIWUUrRFHCfQlcwzvjB9Q_K1vkrSEJCUQDTLqRHU2UEQjr1vhUytcvG7hKX9glUJjoxbSUY8O_1bQYvpZ7TOKLJ9YXI87fsdsCjOCH8pB3fiIxiezlWu0z6nZe6wVVSJFDrDdBem0x4EW9r5DDygdavp_pb5Y0W7eDFR-iX1WCGnPMNjDjpXexXTIdI_Ol2eLqKWFGHW4MUrUqdaqwYDldwTkGvUFz36lUI7bBBSR8z1QvvqnzPopmvsUdYFcp1-fYYTK9hnrhV/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/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.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1pg-D_wLryyZksJTKvQ2XCj2jB5SkB2H8DVHgj5FtQzPyNkniuHdTaL_IBFsxabyNQVwyDAGRDb0cGEIzTIwtcuvIjwV3Lg7QiLDyCU74wL7e7OWYfCCCREmXi9pTrSNypqR7dIGxdS9SqZWfBT2kNZZz3MP8T3iMaDPJB9tUGA0ftI51Y1MpTzJb0BuB7LpTw9riLUlNPvZd3ibg1m7sC629TtuUgdOT-UbH-LxXKgxPhoGJTq0JLzVzIVxqiHbwMlHBsuO84niKNg6mU818Tct_f3UyRX5FTrDYdFHzIsp8PP-5erbf9ISg_MOJtcBAuHtG9F7ocoXiqQITXSSQuw/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/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
