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Apologies, my version and distro are below:

FS: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

OS: Windows via WSL-2

Ben

From: Deck,Benjamin Sent: Thursday, May 19, 2022 4:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Overlapping label files and issue with --ldir in mris_label2annot

Hi there,

Thanks for putting together FS, great software!

I am having trouble running mris_label2annot

Currently I have extracted individually estimated .mgh overlay files from Li 2019 et a., Performing group-level functional image analyses based on homologous functional regions mapped in individuals, software suite in matlab. These individual .mgh files are for every ROI from every one of Yeo 2011's 17 network parcellation scheme.

I then take the .mgh files and convert them into label files with the following script.

if [[ $# -lt 1 ]]; then cat <<USAGE $0 <inDir> <subjects> <SUBJECTS_DIR> inDir - input directory --path to matchrate folder from li 2019 subjects - list of subjects to run SUBJECTS_DIR - Freesurfer SUBJECTS_DIR USAGE exit 1 fi

# echo inputs echo "input 1 is ${1}" echo "input 2 is ${2}" echo "input 3 is ${3}"

# parse inputs inDir=$1 subjects=$2 subDir=$3

networks='Net_10 Net_11 Net_12 Net_13 Net_14 Net_15 Net_16 Net_17 Net_18 Net_19 Net_2 Net_3 Net_4 Net_5 Net_6 Net_7 Net_8 Net_9'

export SUBJECTS_DIR=${subDir} # gather the freesurfer subjects directory

# loop over subjects for sub in ${subjects}; do for net in ${networks}; do

# extract networks masks masks=$(find ${inDir}/Indi_Matched_ROIs/${net}/${sub} -iname '*Net_*.mgh')

# extract confidence masks echo echo -------------------------------------------- echo -- START: creating .cor files ${sub} -- echo -------------------------------------------- echo

# loop over masks for mask in ${masks}; do netMaskName=$(basename ${mask} .mgh) # gather mask name by network number (Yeo 2011) hemi=$(echo ${mask} | grep -Eo '[lr]h') # designate the hemisphere

# resample to native mri_surf2surf --srcsubject fsaverage4 \ --srcsurfval ${mask} \ --trgsubject ${sub} \ --trgsurfval ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${netMaskName}.mgh \ --hemi ${hemi} \ --cortex

mri_vol2label --i ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${netMaskName}.mgh \ --id 1 \ --l ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${netMaskName}.label \ --surf ${sub} ${hemi} white

echo echo -------------------------------------------- echo -- START: creating label files ${sub} -- echo -------------------------------------------- echo

mri_label2label --srclabel ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${netMaskName}.label \ --s ${sub} \ --hemi ${hemi} \ --dilate 2 \ --trglabel ${subDir}/${sub}/label/${sub}_${netMaskName}_dil2.label \ --regmethod surface

done done done

After this script runs to completion, I then run mris_label2annot with the following command

mris_label2annot --s sub-DAEK --hemi rh \ --ctab /mnt/c/Users/Ben/Documents/GitHub/parcellationPipeline/li2019_to_dti/yeo2011nodesLUT.txt \ --a yeo2011nodes \ --surf orig \ --maxstatwinner \ --l Net_10_ROIs_1_rh.label --l Net_11_ROIs_1_rh.label --l Net_12_ROIs_1_rh.label --l Net_12_ROIs_2_rh.label \ --l Net_13_ROIs_1_rh.label --l Net_13_ROIs_2_rh.label --l Net_13_ROIs_3_rh.label --l Net_13_ROIs_4_rh.label \ --l Net_14_ROIs_1_rh.label --l Net_14_ROIs_2_rh.label --l Net_14_ROIs_3_rh.label --l Net_14_ROIs_4_rh.label \ --l Net_14_ROIs_5_rh.label --l Net_15_ROIs_1_rh.label --l Net_16_ROIs_1_rh.label --l Net_16_ROIs_2_rh.label \ --l Net_16_ROIs_3_rh.label --l Net_17_ROIs_1_rh.label --l Net_17_ROIs_2_rh.label --l Net_17_ROIs_3_rh.label \ --l Net_17_ROIs_4_rh.label --l Net_18_ROIs_1_rh.label --l Net_18_ROIs_2_rh.label \ --l Net_18_ROIs_3_rh.label --l Net_18_ROIs_4_rh.label --l Net_19_ROIs_1_rh.label --l Net_2_ROIs_1_rh.label \ --l Net_2_ROIs_2_rh.label --l Net_3_ROIs_1_rh.label --l Net_3_ROIs_2_rh.label --l Net_3_ROIs_3_rh.label \ --l Net_4_ROIs_1_rh.label --l Net_5_ROIs_1_rh.label --l Net_5_ROIs_2_rh.label --l Net_6_ROIs_1_rh.label \ --l Net_6_ROIs_2_rh.label --l Net_6_ROIs_3_rh.label --l Net_7_ROIs_1_rh.label --l Net_7_ROIs_2_rh.label \ --l Net_8_ROIs_1_rh.label --l Net_8_ROIs_2_rh.label --l Net_8_ROIs_3_rh.label --l Net_8_ROIs_4_rh.label \ --l Net_8_ROIs_5_rh.label --l Net_8_ROIs_6_rh.label --l Net_9_ROIs_1_rh.label --l Net_9_ROIs_2_rh.label \ --l Net_9_ROIs_2_rh.label --l Net_9_ROIs_3_rh.label --l Net_9_ROIs_4_rh.label --l Net_9_ROIs_5_rh.label \ --l Net_9_ROIs_6_rh.label --l Net_7_ROIs_3_rh.label

However, the label files are overlapping. Is there a way to fix this, perhaps with some thresholding scheme?

Finally, I also noticed that the -ldir argument from mris_label2annot doesn't seem to be working.

Here is my LUT:

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

0 Unknown 0 0 0 0 1 Net_2_ROIs_1_lh 25 5 25 0 2 Net_2_ROIs_1_rh 25 100 40 0 3 Net_2_ROIs_2_lh 70 130 180 0 4 Net_2_ROIs_2_rh 125 100 160 0 5 Net_3_ROIs_1_lh 196 58 250 0 6 Net_3_ROIs_1_rh 100 25 0 0 7 Net_3_ROIs_2_lh 120 70 50 0 8 Net_3_ROIs_2_rh 220 20 10 0 9 Net_3_ROIs_3_lh 220 20 100 0 10 Net_3_ROIs_3_rh 180 40 120 0 11 Net_4_ROIs_1_lh 122 186 220 0 12 Net_4_ROIs_1_rh 140 20 140 0 13 Net_5_ROIs_1_lh 12 48 255 0 14 Net_5_ROIs_1_rh 20 30 140 0 ............. Etc etc

Thanks, Ben