Re: [Freesurfer] Overlapping label files and issue with --ldir in mris_label2annot

You can combine the labels into an annotation (mris_label2annot), then map the annotation to the new subjects, then break the annot back into labels (mri_annotation2label)

On 5/23/2022 11:55 AM, Deck,Benjamin wrote:

External Email - Use Caution

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

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