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
--Benjamin L. Deck
Doctoral Student
Applied Cognitive and Brain Sciences
Department of Psychological and Brain Sciences
Drexel University
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Applied Cognitive and Brain Sciences
Department of Psychological and Brain Sciences
Drexel University