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
https://secure-web.cisco.com/1Ok_bjRoSx7hgPT1plimaiPInYam-oUdGIluzUE74StkCjzWyu9CoYVWmBB51y-3670jl7ErdMSzpjEJCyx-wfSWToL9bXnJwbT0DkSdvDQNWwngpEGo0ayf1qBf_JqO9Y5WAMTA4Bw6kcPvUvFrLgTPzOofMYal-8rdk90pFpLdMqwuzJxEGtODeRCkyzxCCc5l87QSo6oiR_Lt-GVI0kdirIVWqFcp31KkNw0o2d8ZT6h_yVCIoUDGOEIuU1QDCm--uZ9-2IBXyIim0_bku2N7TFi9JaF76hSkz5GybdVY4kTrpoKkHj2GHsy81fi2O8R9QSu2URTpy1m2ya22wgA/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon Virus-free. http://secure-web.cisco.com/1pqCCuqm-k8y8rQsVXWGpNzQrkCGqMQ1BhF02cgBHR0VLPYG... https://secure-web.cisco.com/1HyWF2aEsq0U_5fH2occEWM4DJJ66hFXrMTljDiMy8wMQgw2g-x2LvpY-vrNwdMv9y_uHWBET1bygPYADXmvdvq6IhfKK5vvxudvyJAFZxPNs-X0e_h2NaZaFWIeEKWVIzI4Z82K9gusG3jpitfrVrcjnWom-gza6YKCcxzvycrxA5Z3edhcI9KqpiUM-PyjhTsIPbLtxAC8Ppgc9LPGld5WwrwpKNfzT7oE_3nXPCBjtGic8SKFGkZfUDGlsOY4eQ3mhRRqGRfyUHsdCepcasVXq0D-I4MJ3BLvFtF1UNbkCVbMXm8sSVLmhO80Sr3K8Mxe4UjsqQYxe91W42e9TnQ/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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 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*
Virus-free. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pqCCuqm-k8y8rQsVXWGpNzQrkCGqMQ1BhF02cgBHR0VLPYG... https://secure-web.cisco.com/1YnAF7HOvTmiAw4b2v-qinSbPinE1DozllhrvyX8ipXNXhb-thlmaEBmlolRCIWAfegACimXAW_BkTVSIDEEa2in3AFLQUtpfPZNTiQctfC0flTReMo9XMAvdDwIZarWtdmZbbF75Dw67966o49yj-LUBYJpWD8BI9wG2whMOLA_8GsieSCesbQ96e0ih9rwnjWfEquKQyEawtcDB9u9Zhrzqgki6oTADMpIApvSP7gqCV34UHHQ-MtRl7ihxzY7a0qMTN6g0OIJkfEIqfFoUlg3l7U_JsbnaeuUtWlkTI5NeSWicV1K1nsc8Sdup79im6SXKKd8JGvTwsx3T9ZDgEQ/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1nIEbcm5JN0w3AjTDG3zcUPOiW3Y8rRZ12nK6T7C_2JYDkN... 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/15B1iqi0JT-6SIOHtJcF-w-4l7tzeCfDDifHK_effgKw7CD... < https://secure-web.cisco.com/15B1iqi0JT-6SIOHtJcF-w-4l7tzeCfDDifHK_effgKw7CD... . 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.
