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- #!/bin/bash
- # Take all localizer 1st-level GLM analysis results, computes and average zstat map
- # for both contrasts of interest, masks them with the given mask image, and thresholds to
- # identify the voxels matching the desired percentile of largest values
- #
- # Usage:
- # code/localizerstats2mask.sh sub-4 VT_roi 90
- set -e
- set -u
- sub=$1
- mask=$2
- percentile=$3
- dsdir="$(readlink -f .)"
- wdir=$(mktemp -d --suffix=localizer2mask)
- trap "rm -rf $wdir" SIGINT SIGTERM
- cd "$wdir"
- # define contrast names
- contrasts=(dummy all ffa ppa eba loc vis ffa_alt ppa_alt eba_alt loc_alt)
- ##combine MNI2T1 and T12BOLD
- #$FSLDIR/bin/convert_xfm \
- # -omat mni2bold.mat \
- # -concat ${dsdir}/src/tnt/${sub}/t1w/in_bold/xfm_6dof.mat \
- # ${dsdir}/src/tnt/${sub}/t1w/in_mni152/tmpl2subj.mat
- ## re-slice mask
- #$FSLDIR/bin/flirt \
- # -in "${dsdir}/${mask}" \
- # -ref ${dsdir}/src/tnt/${sub}/bold/brain \
- # -applyxfm -init mni2bold.mat \
- # -out mask \
- # -interp nearestneighbour
- ## apply transformation to subject template for all runs
- #for f in ${dsdir}/${sub}/run-*.feat; do
- # $FSLDIR/bin/featregapply "$f"
- # # make zstats
- # $FSLDIR/bin/fslmaths $f/reg_standard/stats/varcope1 -sqrt $f/reg_standard/stats/stdcope1
- # $FSLDIR/bin/fslmaths $f/reg_standard/stats/varcope2 -sqrt $f/reg_standard/stats/stdcope2
- # $FSLDIR/bin/fslmaths $f/reg_standard/stats/cope1 -div $f/reg_standard/stats/stdcope1 $f/reg_standard/stats/zstat1
- # $FSLDIR/bin/fslmaths $f/reg_standard/stats/cope2 -div $f/reg_standard/stats/stdcope2 $f/reg_standard/stats/zstat2
- #done
- # make average zstat across all runs -- mask
- for i in $(seq 10); do
- $FSLDIR/bin/fslmerge -t zstat${i}_merged ${dsdir}/${sub}/run-*.feat/stats/zstat${i}.nii*
- #$FSLDIR/bin/fslmaths zstat${i}_merged -Tmean -mas mask zstat${i}
- $FSLDIR/bin/fslmaths zstat${i}_merged -Tmean zstat${i}
- # take desired upper percentile and threshold for mask
- fslmaths zstat${i} \
- -thr $($FSLDIR/bin/fslstats zstat${i} -P "$percentile") \
- ${dsdir}/${sub}/${contrasts[$i]}_thr${percentile}
- done
- cd -
- rm -rf "$wdir"
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