External Email - Use Caution
Hi Yujing,
Thanks for your continued support on this issue.
Addressing your first question.
If I use --offset 1 then the get the following:
cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --offset 1 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 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 *50 791413 cluster50* Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot
Where cluster50 is some nondescript cluster and it ignores my network 10 which should be the first entry.
To address your second question about duplicates.
*19 3988500 Net_17_ROIs_3_lh_native*
*20 3988540 Net_17_ROIs_4_lh_native*
While these may look almost like duplicates they are different rois within the same larger network. This separation is important for what I am doing so I need to keep the ROIs separate from one another but they are a part of the same larger network. However, Freesurfer doesn't know that they are.
On Thu, Jun 23, 2022 at 10:17 AM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
I am confused about ‘—no-unknown –offset 0’. Your output doesn’t seem agree with the codes. If your label starts at 1, I think it should be ‘—offset 1’ instead of 0. Can you double check your LUT?
I see duplicates in second column of these lines: (second column is calculated from RGB values.)
19 3988500 Net_17_ROIs_3_lh_native
20 3988540 Net_17_ROIs_4_lh_native
22 9221340 Net_18_ROIs_2_lh_native
23 3302420 Net_18_ROIs_3_lh_native
28 1326300 Net_2_ROIs_2_lh_native
29 3957880 Net_3_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
48 1326300 Net_9_ROIs_2_lh_native
49 3957880 Net_9_ROIs_3_lh_native
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck *Sent:* Thursday, June 23, 2022 9:36 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
External Email - Use Caution *Hi Yujing,
I am not seeing any duplicates--highlighting wasn't rendered on my end.
my 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
which is why I gave the --offset flag as 0 for --no-unknown
I did notice that the labels is incorrect. So for some reason, it seems to be missing two labels that exist in the annotation. That is strange.
Ben
On Thu, Jun 23, 2022 at 8:55 AM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
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.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.edu < 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.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.com wrote:
Hi Yujing,
Thank you. I will give it a try! Can documentation be updated?
Ben
Virus-free. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/12Pr5R9OUs3m5tmfVFiR-G7DLc9-DpQ-0CKGmcCq4i_I5Mjt... https://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.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.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.edu < 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.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
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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing 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.edu < 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.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
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*Department of Psychological and Brain Sciences*
*Drexel University*
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*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://secure-web.cisco.com/1-Co0Tj3nO9PKVc4FF5EYp-pbwW1MSBhpVRo4lPgCIr_Le-... 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/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QL... < https://secure-web.cisco.com/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QL... . 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.
