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Wow, amazing. That worked!!
Thanks a ton!! Ben
On Jun 9, 2022, at 2:50 PM, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
Hi Ben,
Sorry, I didn’t make it clear. Remove hemi from your LUT.
Hope it works this time.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 CautionHi 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 YHUANG43@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] vertex out of range mris_label2annot
External Email - Use CautionOh 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 YHUANG43@mgh.harvard.edu wrote: Sorry, I meant the command that you ran with --ldir flag and generated empty annotation file.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] vertex out of range mris_label2annot
External Email - Use CautionHi 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 YHUANG43@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] vertex out of range mris_label2annot
External Email - Use CautionOh, 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 YHUANG43@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: [Freesurfer] vertex out of range mris_label2annot
External Email - Use CautionHi 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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-- 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://secure-web.cisco.com/1taIQlr3H_Ns5U3lYk6wY5aT9CD81GQuAspXcWQnZDnVaDn... 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://secure-web.cisco.com/1ORzHzR78Uml52rJ8sBGRqlPw0XtFeMGIX3YQBselZNzE3M... <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ORzHzR78Uml52rJ8sBGRqlPw0XtFeMGIX3YQBselZNzE3M... . 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 https://secure-web.cisco.com/1taIQlr3H_Ns5U3lYk6wY5aT9CD81GQuAspXcWQnZDnVaDn... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1ORzHzR78Uml52rJ8sBGRqlPw0XtFeMGIX3YQBselZNzE3M... https://secure-web.cisco.com/1ORzHzR78Uml52rJ8sBGRqlPw0XtFeMGIX3YQBselZNzE3MOwByYGhRHd-n8rIZ9E9qJXhE3klNKu4BOmFipOs3ejs0lO4BKYAzyOwnJDx5hcJpDYyC1WkC-mFGr3UpuZrhQ5CCjo_FyRL_ta_iPFJi4OegiJ0ENiPWqoJWKRERgYls1b3PWJKDJc8YGK9xG2-C4Sstg5Ml0GoT8vX7OuDiHwLGyhgiq6sThTeX6jKo4xf0ENThVedueMb1KUPh8lFW9YiEvnCARuovy-BVnPS5vb4e7TKiFOB7KmYYFscG0c9xYn8h0mxxzOum5Y8GgE/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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.
