Apologies, my version and distro are below:

 

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

 

OS: Windows via WSL-2

 

Ben

 

 

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