Hi Ben,

Sorry, I didn’t make it clear. Remove hemi from your LUT.

Hope it works this time.

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck
Sent: Thursday, June 9, 2022 2:41 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] vertex out of range mris_label2annot


        External Email - Use Caution
Hi Yujing,

I tried with a couple labels and a new LUT.

command :

mris_label2annot --s sub-DAEK --h lh --a test --ldir 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/test_labels --ctab 
/mnt/c/Users/Ben/Documents/GitHub/parcellationPipeline/li2019_to_dti/test_lut.txt
 --maxstatwinner

label files:
lh.Net_13_ROIs_1_lh_native_dil2.label
lh.Net_13_ROIs_2_lh_native_dil2.label
lh.Net_13_ROIs_3_lh_native_dil2.label
lh.Net_13_ROIs_4_lh_native_dil2.label
lh.Net_13_ROIs_5_lh_native_dil2.label

LUT:

#
#No. Label Name:                            R   G   B   A
#

0  Unknown                                       0   0   0   0
1 lh.Net_13_ROIs_1_lh_native_dil2                        122 135 50  0
2 rh.Net_13_ROIs_1_rh_native_dil2                        0 192 32  0
3 lh.Net_13_ROIs_2_lh_native_dil2                        115 145 90  0
4 rh.Net_13_ROIs_2_rh_native_dil2                        125 100 10  0
5 lh.Net_13_ROIs_3_lh_native_dil2                        20  90  0   0
6 rh.Net_13_ROIs_3_rh_native_dil2                        0   100 60  0
7 lh.Net_13_ROIs_4_lh_native_dil2                        122 135 50  0
8 rh.Net_13_ROIs_4_rh_native_dil2                        80  40  20  0
9 lh.Net_13_ROIs_5_lh_native_dil2                        122 0   50  0
10 rh.Net_13_ROIs_5_rh_native_dil2                        100 135 100 0
11 lh.Net_13_ROIs_6_lh_native_dil2                        0   100 60  0


Still not sure why --ldir isn't working.

  freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

Ben


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On Thu, Jun 9, 2022 at 12:15 PM Huang, Yujing 
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi Ben,

I checked mris_label2annot implementation. It seems that it is expecting the 
label files as [hemi].[label-name].label in –ldir directory. The label-name 
needs to match what is specified in your LUT.

If you would like to see if it works, it might be a good idea to create a new 
directory and put just a couple of renamed label files there.

Hope this helps.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Benjamin Deck
Sent: Thursday, June 9, 2022 11:11 AM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] vertex out of range mris_label2annot


        External Email - Use Caution
Oh apologies for the crossed-wires

Sure, command:

mris_label2annot  --s sub-DAEK \
--hemi lh \
--ctab 
/mnt/c/Users/Ben/Documents/GitHub/parcellationPipeline/li2019_to_dti/yeo2011nodesLUT.txt
 \
--a yeo2011nodes \
--maxstatwinner  \
--ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels

Thanks,
Ben

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On Thu, Jun 9, 2022 at 11:08 AM Huang, Yujing 
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
Sorry, I meant the command that you ran with --ldir flag and generated empty 
annotation file.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Benjamin Deck
Sent: Thursday, June 9, 2022 10:58 AM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] vertex out of range mris_label2annot


        External Email - Use Caution
Hi Yujing,

Sure thing.

Full command:

mris_label2annot  --s sub-DAEK --hemi lh --ctab 
/mnt/c/Users/Ben/Documents/GitHub/parcellationPipeline/li2019_to_dti/yeo2011nodesLUT.txt
 --a yeo2011nodes --maxstatwinner --l Net_10_ROIs_1_lh_native_dil2 --l 
Net_10_ROIs_1_rh_native_dil2 --l Net_11_ROIs_1_lh_native_dil2 --l 
Net_11_ROIs_1_rh_native_dil2  --l Net_12_ROIs_1_lh_native_dil2 --l 
Net_12_ROIs_1_rh_native_dil2 --l Net_12_ROIs_2_lh_native_dil2 --l 
Net_12_ROIs_2_rh_native_dil2 --l Net_13_ROIs_1_lh_native_dil2 --l 
Net_13_ROIs_1_rh_native_dil2 --l Net_13_ROIs_2_lh_native_dil2 --l 
Net_13_ROIs_2_rh_native_dil2 --l Net_13_ROIs_3_lh_native_dil2 --l 
Net_13_ROIs_3_rh_native_dil2 --l Net_13_ROIs_4_lh_native_dil2 --l 
Net_13_ROIs_4_rh_native_dil2 --l Net_13_ROIs_5_lh_native_dil2 --l 
Net_14_ROIs_1_lh_native_dil2 --l Net_14_ROIs_1_rh_native_dil2 --l 
Net_14_ROIs_2_lh_native_dil2 --l Net_14_ROIs_2_rh_native_dil2 --l 
Net_14_ROIs_3_lh_native_dil2 --l Net_14_ROIs_3_rh_native_dil2 --l 
Net_14_ROIs_4_lh_native_dil2 --l Net_14_ROIs_4_rh_native_dil2 --l 
Net_14_ROIs_5_lh_native_dil2 --l Net_14_ROIs_5_rh_native_dil2 --l 
Net_15_ROIs_1_lh_native_dil2 --l Net_15_ROIs_1_rh_native_dil2 --l 
Net_16_ROIs_1_lh_native_dil2 --l Net_16_ROIs_1_rh_native_dil2 --l 
Net_16_ROIs_2_lh_native_dil2 --l Net_16_ROIs_2_rh_native_dil2 --l 
Net_16_ROIs_3_rh_native_dil2 --l Net_17_ROIs_1_lh_native_dil2 --l 
Net_17_ROIs_1_rh_native_dil2 --l Net_17_ROIs_2_lh_native_dil2 --l 
Net_17_ROIs_2_rh_native_dil2 --l Net_17_ROIs_3_lh_native_dil2 --l 
Net_17_ROIs_3_rh_native_dil2 --l Net_17_ROIs_4_lh_native_dil2 --l 
Net_17_ROIs_4_rh_native_dil2 --l Net_18_ROIs_1_lh_native_dil2 --l 
Net_18_ROIs_1_rh_native_dil2 --l Net_18_ROIs_2_lh_native_dil2 --l 
Net_18_ROIs_2_rh_native_dil2 --l Net_18_ROIs_3_lh_native_dil2 --l 
Net_18_ROIs_3_rh_native_dil2 --l Net_18_ROIs_4_lh_native_dil2 --l 
Net_18_ROIs_4_rh_native_dil2 --l Net_18_ROIs_5_lh_native_dil2 --l 
Net_19_ROIs_1_lh_native_dil2 --l Net_19_ROIs_1_rh_native_dil2 --l 
Net_2_ROIs_1_lh_native_dil2 --l Net_2_ROIs_1_rh_native_dil2 --l 
Net_2_ROIs_2_lh_native_dil2 --l Net_2_ROIs_2_rh_native_dil2 --l 
Net_3_ROIs_1_lh_native_dil2 --l Net_3_ROIs_1_rh_native_dil2 --l 
Net_3_ROIs_2_lh_native_dil2 --l Net_3_ROIs_2_rh_native_dil2 --l 
Net_3_ROIs_3_lh_native_dil2 --l Net_3_ROIs_3_rh_native_dil2 --l 
Net_4_ROIs_1_lh_native_dil2 --l Net_4_ROIs_1_rh_native_dil2 --l 
Net_5_ROIs_1_lh_native_dil2 --l Net_5_ROIs_1_rh_native_dil2 --l 
Net_5_ROIs_2_lh_native_dil2 --l Net_5_ROIs_2_rh_native_dil2 --l 
Net_5_ROIs_3_lh_native_dil2 --l Net_5_ROIs_3_rh_native_dil2 --l 
Net_5_ROIs_4_lh_native_dil2 --l Net_5_ROIs_4_rh_native_dil2 --l 
Net_6_ROIs_1_lh_native_dil2 --l Net_6_ROIs_1_rh_native_dil2 --l 
Net_6_ROIs_2_lh_native_dil2 --l Net_6_ROIs_2_rh_native_dil2 --l 
Net_6_ROIs_3_lh_native_dil2 --l Net_6_ROIs_3_rh_native_dil2 --l 
Net_7_ROIs_1_lh_native_dil2 --l Net_7_ROIs_1_rh_native_dil2 --l 
Net_7_ROIs_2_lh_native_dil2 --l Net_7_ROIs_2_rh_native_dil2 --l 
Net_7_ROIs_3_rh_native_dil2 --l Net_8_ROIs_1_lh_native_dil2 --l 
Net_8_ROIs_1_rh_native_dil2 --l Net_8_ROIs_2_lh_native_dil2 --l 
Net_8_ROIs_2_rh_native_dil2 --l Net_8_ROIs_3_lh_native_dil2 --l 
Net_8_ROIs_3_rh_native_dil2 --l Net_8_ROIs_4_lh_native_dil2 --l 
Net_8_ROIs_4_rh_native_dil2 --l Net_8_ROIs_5_lh_native_dil2 --l 
Net_8_ROIs_5_rh_native_dil2 --l Net_8_ROIs_6_rh_native_dil2 --l 
Net_9_ROIs_1_lh_native_dil2 --l Net_9_ROIs_1_rh_native_dil2 --l 
Net_9_ROIs_2_lh_native_dil2 --l Net_9_ROIs_2_rh_native_dil2 --l 
Net_9_ROIs_3_lh_native_dil2 --l Net_9_ROIs_3_rh_native_dil2 --l 
Net_9_ROIs_4_rh_native_dil2 --l Net_9_ROIs_5_rh_native_dil2 --l 
Net_9_ROIs_6_rh_native_dil2


You might need my LUT also----See attached. --I can also send you the label 
files if you need me to.

Thanks for your help!

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On Thu, Jun 9, 2022 at 10:33 AM Huang, Yujing 
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
Can you provide the full command that you were having trouble? I would like to 
see if I can reproduce here.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Benjamin Deck
Sent: Thursday, June 9, 2022 10:11 AM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] vertex out of range mris_label2annot


        External Email - Use Caution
Oh, that makes sense, as my --hemi flag is lh.

However, when I run the same command with --ldir and the ctab LUT the --ldir 
flag doesn't ID any of my label files. Therefore, I have to provide the --l 
flags, otherwise it just creates an empty annotation file.

Ben

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On Thu, Jun 9, 2022 at 8:57 AM Huang, Yujing 
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi Benjamin,

The error indicates that a label in Net_10_ROIs_1_rh_native_dil2.label has 
vertex 254077 that is outside lh.orig.

I’m wondering how you created those label files.

Best,

Yujing




From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Benjamin Deck
Sent: Monday, June 6, 2022 4:06 PM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] vertex out of range mris_label2annot


        External Email - Use Caution
Hi freesurfer experts,

I am attempting to create a custom annotation file with the following LUT and 
call:

mris_label2annot  --s sub-DAEK --hemi lh \
--ctab sub-DAEK_yeoLUT.txt \
--a yeo2011nodes \
--maxstatwinner \
--l  Net_10_ROIs_1_lh_native_dil2.label \
--l  Net_10_ROIs_1_rh_native_dil2.label \
--l  Net_11_ROIs_1_lh_native_dil2.label \
--l  Net_11_ROIs_1_rh_native_dil2.label \
--l  Net_12_ROIs_1_lh_native_dil2.label \
--l  Net_12_ROIs_1_rh_native_dil2.label \
--l  Net_12_ROIs_2_lh_native_dil2.label \
.....many other labels


LUT:

0 Unknown 0 0 0 0
1 Net_10_ROIs_1_lh_native 5   5   5   0
2 Net_10_ROIs_1_rh_native 25  5   25  0
3 Net_11_ROIs_1_lh_native 25  100 40  0
4 Net_11_ROIs_1_rh_native 70  130 180 0
5 Net_12_ROIs_1_lh_native 100 100 0   0
6 Net_12_ROIs_1_rh_native 196 58  250 0
.....many others

However, when I run the above command it breaks with the following issue:


Reading ctab sub-DAEK_yeoLUT.txt
Number of ctab entries 104

7.2.0
cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels
cmdline mris_label2annot --s sub-DAEK --hemi lh --ctab sub-DAEK_yeoLUT.txt --a 
yeo2011nodes --maxstatwinner --l Net_10_ROIs_1_lh_native_dil2.label --l 
Net_10_ROIs_1_rh_native_dil2.label --l Net_11_ROIs_1_lh_native_dil2.label --l 
Net_11_ROIs_1_rh_native_dil2.label --l Net_12_ROIs_1_lh_native_dil2.label --l 
Net_12_ROIs_1_rh_native_dil2.label --l Net_12_ROIs_2_lh_native_dil2.label --l 
Net_12_ROIs_2_rh_native_dil2.label --l Net_13_ROIs_1_lh_native_dil2.label --l 
Net_13_ROIs_1_rh_native_dil2.label --l Net_13_ROIs_2_lh_native_dil2.label --l 
Net_13_ROIs_2_rh_native_dil2.label --l Net_13_ROIs_3_lh_native_dil2.label --l 
Net_13_ROIs_3_rh_native_dil2.label --l Net_13_ROIs_4_lh_native_dil2.label --l 
Net_13_ROIs_4_rh_native_dil2.label --l Net_13_ROIs_5_lh_native_dil2.label --l 
Net_14_ROIs_1_lh_native_dil2.label --l Net_14_ROIs_1_rh_native_dil2.label --l 
Net_14_ROIs_2_lh_native_dil2.label --l Net_14_ROIs_2_rh_native_dil2.label --l 
Net_14_ROIs_3_lh_native_dil2.label --l Net_14_ROIs_3_rh_native_dil2.label --l 
Net_14_ROIs_4_lh_native_dil2.label --l Net_14_ROIs_4_rh_native_dil2.label --l 
Net_14_ROIs_5_lh_native_dil2.label --l Net_14_ROIs_5_rh_native_dil2.label --l 
Net_15_ROIs_1_lh_native_dil2.label --l Net_15_ROIs_1_rh_native_dil2.label --l 
Net_16_ROIs_1_lh_native_dil2.label --l Net_16_ROIs_1_rh_native_dil2.label --l 
Net_16_ROIs_2_lh_native_dil2.label --l Net_16_ROIs_2_rh_native_dil2.label --l 
Net_16_ROIs_3_rh_native_dil2.label --l Net_17_ROIs_1_lh_native_dil2.label --l 
Net_17_ROIs_1_rh_native_dil2.label --l Net_17_ROIs_2_lh_native_dil2.label --l 
Net_17_ROIs_2_rh_native_dil2.label --l Net_17_ROIs_3_lh_native_dil2.label --l 
Net_17_ROIs_3_rh_native_dil2.label --l Net_17_ROIs_4_lh_native_dil2.label --l 
Net_17_ROIs_4_rh_native_dil2.label --l Net_18_ROIs_1_lh_native_dil2.label --l 
Net_18_ROIs_1_rh_native_dil2.label --l Net_18_ROIs_2_lh_native_dil2.label --l 
Net_18_ROIs_2_rh_native_dil2.label --l Net_18_ROIs_3_lh_native_dil2.label --l 
Net_18_ROIs_3_rh_native_dil2.label --l Net_18_ROIs_4_lh_native_dil2.label --l 
Net_18_ROIs_4_rh_native_dil2.label --l Net_18_ROIs_5_lh_native_dil2.label --l 
Net_19_ROIs_1_lh_native_dil2.label --l Net_19_ROIs_1_rh_native_dil2.label --l 
Net_2_ROIs_1_lh_native_dil2.label --l Net_2_ROIs_1_rh_native_dil2.label --l 
Net_2_ROIs_2_lh_native_dil2.label --l Net_2_ROIs_2_rh_native_dil2.label --l 
Net_3_ROIs_1_lh_native_dil2.label --l Net_3_ROIs_1_rh_native_dil2.label --l 
Net_3_ROIs_2_lh_native_dil2.label --l Net_3_ROIs_2_rh_native_dil2.label --l 
Net_3_ROIs_3_lh_native_dil2.label --l Net_3_ROIs_3_rh_native_dil2.label --l 
Net_4_ROIs_1_lh_native_dil2.label --l Net_4_ROIs_1_rh_native_dil2.label --l 
Net_5_ROIs_1_lh_native_dil2.label --l Net_5_ROIs_1_rh_native_dil2.label --l 
Net_5_ROIs_2_lh_native_dil2.label --l Net_5_ROIs_2_rh_native_dil2.label --l 
Net_5_ROIs_3_lh_native_dil2.label --l Net_5_ROIs_3_rh_native_dil2.label --l 
Net_5_ROIs_4_lh_native_dil2.label --l Net_5_ROIs_4_rh_native_dil2.label --l 
Net_6_ROIs_1_lh_native_dil2.label --l Net_6_ROIs_1_rh_native_dil2.label --l 
Net_6_ROIs_2_lh_native_dil2.label --l Net_6_ROIs_2_rh_native_dil2.label --l 
Net_6_ROIs_3_lh_native_dil2.label --l Net_6_ROIs_3_rh_native_dil2.label --l 
Net_7_ROIs_1_lh_native_dil2.label --l Net_7_ROIs_1_rh_native_dil2.label --l 
Net_7_ROIs_2_lh_native_dil2.label --l Net_7_ROIs_2_rh_native_dil2.label --l 
Net_7_ROIs_3_rh_native_dil2.label --l Net_8_ROIs_1_lh_native_dil2.label --l 
Net_8_ROIs_1_rh_native_dil2.label --l Net_8_ROIs_2_lh_native_dil2.label --l 
Net_8_ROIs_2_rh_native_dil2.label --l Net_8_ROIs_3_lh_native_dil2.label --l 
Net_8_ROIs_3_rh_native_dil2.label --l Net_8_ROIs_4_lh_native_dil2.label --l 
Net_8_ROIs_4_rh_native_dil2.label --l Net_8_ROIs_5_lh_native_dil2.label --l 
Net_8_ROIs_5_rh_native_dil2.label --l Net_8_ROIs_6_rh_native_dil2.label --l 
Net_9_ROIs_1_lh_native_dil2.label --l Net_9_ROIs_1_rh_native_dil2.label --l 
Net_9_ROIs_2_lh_native_dil2.label --l Net_9_ROIs_2_rh_native_dil2.label --l 
Net_9_ROIs_3_lh_native_dil2.label --l Net_9_ROIs_3_rh_native_dil2.label --l 
Net_9_ROIs_4_rh_native_dil2.label --l Net_9_ROIs_5_rh_native_dil2.label --l 
Net_9_ROIs_6_rh_native_dil2.label
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  yeo2011nodes
nlables 104
LabelThresh 0 0.000000
Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig
 1 328965 Net_10_ROIs_1_lh_native
 2 1639705 Net_10_ROIs_1_rh_native
WARNING: vertex 210080 maps to multiple labels! (overwriting)
WARNING: vertex 210124 maps to multiple labels! (overwriting)
WARNING: vertex 210125 maps to multiple labels! (overwriting)
WARNING: vertex 210151 maps to multiple labels! (overwriting)
WARNING: vertex 210172 maps to multiple labels! (overwriting)
WARNING: vertex 210173 maps to multiple labels! (overwriting)
WARNING: vertex 211157 maps to multiple labels! (overwriting)
WARNING: vertex 211158 maps to multiple labels! (overwriting)
ERROR: Net_10_ROIs_1_rh_native_dil2.label, n=9538, vertex 254077 out of range


Any thoughts on the fix for this issue?

Thanks



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