Re: [Freesurfer] vertex out of range mris_label2annot

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 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 <YHUANG43@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University