‘35 11223921 cluster35’ is randomly generated color scheme from mris_label2annot.
Not sure how you ran mri_annotation2label. But it looks like you are missing label file for corpuscallosum. The output should be correct if you fix that.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Benjamin Deck
Sent: Monday, June 27, 2022 10:42 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
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Hi Yujing,
Sorry. I broke apart the annotation file to get the labels using mri_annotation2label. Then simply tried to reconstruct it.
Ben
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On Mon, Jun 27, 2022 at 10:31 AM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:
Hi Ben,
Sorry for all the troubles.
I’m trying to reproduce here. I found aparc.annot.ctab in bert directory. I have a question about the label files. Are they part of the tutorial data? Where did you download the data? I don’t see those label files in the directory.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck
Sent: Sunday, June 26, 2022 3:02 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
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So I thought that since this has caused me many issues I would test this on the bert subject using aparc.annot. These are default with freesurfer.
command using Bert:
cwd /mnt/c/Users/Ben/freesurfer/subjects/bert/label
cmdline mris_label2annot --s bert --hemi lh --ctab /mnt/c/Users/Ben/freesurfer/subjects/bert/label/aparc.annot.ctab --a myaparc --ldir /mnt/c/Users/Ben/freesurfer/subjects/bert/label/
sysname Linux
hostname LAPTOP-LPS9CH5E
machine x86_64
user bdeck8317
subject bert
hemi lh
SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects
ColorTable /mnt/c/Users/Ben/freesurfer/subjects/bert/label/aparc.annot.ctab
AnnotName myaparc
nlables 35
LabelThresh 0 0.000000
Loading /mnt/c/Users/Ben/freesurfer/subjects/bert/surf/lh.orig
1 2647065 bankssts
2 10511485 caudalanteriorcingulate
3 6500 caudalmiddlefrontal
4 6558940 cuneus
5 660700 entorhinal
6 9231540 fusiform
7 14433500 inferiorparietal
8 7874740 inferiortemporal
9 9180300 isthmuscingulate
10 9182740 lateraloccipital
11 3296035 lateralorbitofrontal
12 9211105 lingual
13 4924360 medialorbitofrontal
14 3302560 middletemporal
15 3988500 parahippocampal
16 3988540 paracentral
17 9221340 parsopercularis
18 3302420 parsorbitalis
19 1326300 parstriangularis
20 3957880 pericalcarine
21 1316060 postcentral
22 14464220 posteriorcingulate
23 14423100 precentral
24 11832480 precuneus
25 9180240 rostralanteriorcingulate
26 8204875 rostralmiddlefrontal
27 10542100 superiorfrontal
28 9221140 superiorparietal
29 14474380 superiortemporal
30 1351760 supramarginal
31 6553700 frontalpole
32 11146310 temporalpole
33 13145750 transversetemporal
34 2146559 insula
35 11223921 cluster35
Mapping unhit to unknown
Found 0 unhit vertices
Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/bert/label/lh.myaparc.annot_____________________________________________________________________
It seems to be not indexing properly into the CTAB file
CTAB:
0 unknown 25 5 25 0
1 bankssts 25 100 40 0
2 caudalanteriorcingulate 125 100 160 0
3 caudalmiddlefrontal 100 25 0 0
4 corpuscallosum 120 70 50 0
5 cuneus 220 20 100 0
6 entorhinal 220 20 10 0
7 fusiform 180 220 140 0
8 inferiorparietal 220 60 220 0
9 inferiortemporal 180 40 120 0
10 isthmuscingulate 140 20 140 0
11 lateraloccipital 20 30 140 0
12 lateralorbitofrontal 35 75 50 0
13 lingual 225 140 140 0
14 medialorbitofrontal 200 35 75 0
15 middletemporal 160 100 50 0
16 parahippocampal 20 220 60 0
17 paracentral 60 220 60 0
18 parsopercularis 220 180 140 0
19 parsorbitalis 20 100 50 0
20 parstriangularis 220 60 20 0
21 pericalcarine 120 100 60 0
22 postcentral 220 20 20 0
23 posteriorcingulate 220 180 220 0
24 precentral 60 20 220 0
25 precuneus 160 140 180 0
26 rostralanteriorcingulate 80 20 140 0
27 rostralmiddlefrontal 75 50 125 0
28 superiorfrontal 20 220 160 0
29 superiorparietal 20 180 140 0
30 superiortemporal 140 220 220 0
31 supramarginal 80 160 20 0
32 frontalpole 100 0 100 0
33 temporalpole 70 20 170 0
34 transversetemporal 150 150 200 0
35 insula 255 192 32 0
I really have no idea why it returns this nondescript cluster 35--- there shouldn't be a cluster 35.
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On Fri, Jun 24, 2022 at 5:10 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:
I noticed two things:
1. you have skipped numbers in label files output - make sure all label names in LUT have corresponding label files hemi.label-name.label in ldir directory.
2. your annotation output doesn’t agree with the LUT your showed - make sure you are passing the correct copy to mris_label2annot
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck
Sent: Friday, June 24, 2022 4:47 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
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Hi Yujing,
I just re-ran this and I am now noticing something else that is strange.
I included an "unknown 0 0 0 0" row at the beginning and gave this a 0 index. Similar to the default LUT
LUT:
0 Unknown 255 255 255 0
1 Net_14_ROIs_4_native 25 5 25 0
2 Net_9_ROIs_1_native 25 100 40 0
3 Net_18_ROIs_4_native 70 130 180 0
My command and output:
mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ctab sub-DAEK_yeoLUT.txt --maxstatwinner --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019/
Reading ctab sub-DAEK_yeoLUT.txt
Number of ctab entries 57
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//lh.Net_14_ROIs_4_native.label
2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_1_native.label
3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_4_native.label
4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_1_native.label
5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_1_native.label
7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_2_native.label
8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_1_native.label
10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_2_native.label
11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_3_native.label
12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_3_native.label
13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_10_ROIs_1_native.label
14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_3_native.label
15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_16_ROIs_2_native.label
16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_4_native.label
17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_3_native.label
18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_3_native.label
20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_2_native.label
21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_2_ROIs_1_native.label
23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_1_native.label
24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_1_native.label
25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_4_native.label
26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_3_native.label
27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_2_native.label
28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_5_native.label
29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_2_native.label
30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_12_ROIs_1_native.label
31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_3_native.label
32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_1_native.label
33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_11_ROIs_1_native.label
35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_2_native.label
36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_2_native.label
37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_4_native.label
39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_15_ROIs_1_native.label
40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_7_ROIs_1_native.label
41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_2_native.label
42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_19_ROIs_1_native.label
43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_2_ROIs_2_native.label
44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_2_native.label
45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_16_ROIs_1_native.label
46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_5_native.label
47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_5_native.label
48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_1_native.label
49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_7_ROIs_2_native.label
50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_12_ROIs_2_native.label
51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_5_native.label
52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_4_native.label
53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_4_ROIs_1_native.label
54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_1_native.label
55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_3_native.label
56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_3_native.label
7.2.0
cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019
cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ctab sub-DAEK_yeoLUT.txt --maxstatwinner --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019/
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
1 2647065 Net_9_ROIs_1_native
2 11829830 Net_18_ROIs_4_native
3 25700 Net_8_ROIs_1_native
4 16399044 Net_14_ROIs_1_native
5 3294840 Net_14_ROIs_2_native
6 660700 Net_6_ROIs_1_native
7 7874740 Net_9_ROIs_2_native
8 14465658 Net_8_ROIs_3_native
9 9180300 Net_17_ROIs_3_native
10 12300 Net_10_ROIs_1_native
11 9182740 Net_5_ROIs_3_native
12 3296035 Net_16_ROIs_2_native
13 9211105 Net_5_ROIs_4_native
14 4924360 Net_9_ROIs_3_native
15 3302560 Net_18_ROIs_3_native
16 3988540 Net_13_ROIs_2_native
17 13777468 Net_2_ROIs_1_native
18 3302420 Net_5_ROIs_1_native
19 3294765 Net_13_ROIs_1_native
20 14443610 Net_8_ROIs_4_native
21 10511400 Net_13_ROIs_3_native
22 8323072 Net_8_ROIs_2_native
23 1326300 Net_18_ROIs_5_native
24 3957880 Net_17_ROIs_2_native
25 1316060 Net_12_ROIs_1_native
26 14464220 Net_3_ROIs_3_native
27 8323072 Net_18_ROIs_1_native
28 7874740 Net_11_ROIs_1_native
29 8860211 Net_3_ROIs_2_native
30 9182740 Net_6_ROIs_2_native
31 3296035 Net_13_ROIs_4_native
32 4924360 Net_15_ROIs_1_native
33 3302560 Net_7_ROIs_1_native
34 3988500 Net_18_ROIs_2_native
35 3988540 Net_19_ROIs_1_native
36 9221340 Net_2_ROIs_2_native
37 3302420 Net_5_ROIs_2_native
38 3302620 Net_16_ROIs_1_native
39 10811612 Net_14_ROIs_5_native
40 2637020 Net_13_ROIs_5_native
41 1326300 Net_3_ROIs_1_native
42 3957880 Net_7_ROIs_2_native
43 1316060 Net_12_ROIs_2_native
44 14464220 Net_8_ROIs_5_native
45 14423100 Net_17_ROIs_4_native
46 11832480 Net_4_ROIs_1_native
47 9180240 Net_17_ROIs_1_native
48 8204875 Net_14_ROIs_3_native
49 10542100 Net_6_ROIs_3_native
50 3840729 cluster50
Mapping unhit to unknown
Found 19023 unhit vertices
Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot
For some very weird reason it skips my 0 row, 'unknown' and then adds an undescript cluster at the end.
Why is that occurring?
Ben
On Fri, Jun 24, 2022 at 4:00 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:
Hi Ben,
Based on your command line options (‘—no-unknown –offset 0’) and output, I believe your LUT starts with ‘0 Net_10_ROIs_1_lh_native 255 255 255 0’ not ‘0 Unknown 0 0 0 0’. Can you double check the LUT you passed to mris_label2annot?
I was able to reproduce the crash with duplicated color scheme scenario. Once you fix duplicated color schemes in your LUT, ‘mris_label2vol –fill-ribbon’ should run fine.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck
Sent: Thursday, June 23, 2022 10:42 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
External Email - Use Caution
Hmm.. I see what you're saying not the names but the actual location. Shouldn't I be getting a warning of overlapping labels and therefore an arg like --maxstatwinner would be helpful?
On Thu, Jun 23, 2022 at 10:34 AM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:
For the duplicates, 19 is same as 41, 20 is same as 42, …
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck
Sent: Thursday, June 23, 2022 10:27 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 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
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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
--Benjamin L. Deck
Doctoral Student
Applied Cognitive and Brain Sciences
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
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Applied Cognitive and Brain Sciences
Department of Psychological and Brain Sciences
Drexel University
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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.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .
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.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .
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.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .
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.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .
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