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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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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Doctoral Student
Applied Cognitive and Brain Sciences
Department of Psychological and Brain Sciences
Drexel University
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