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- #!/bin/bash
- set -e
- set -u
- odir="qa/tsnr/bold3Tp2"
- mkdir -p $odir
- for s in sub-*; do
- echo "$s"
- $FSLDIR/bin/fslmerge -t $odir/${s}_alltsnr $s/in_bold3Tp2/${s}_*_bold_tsnr.nii.gz
- $FSLDIR/bin/fslmaths $odir/${s}_alltsnr -Tmean $odir/${s}_avgtsnr
- $FSLDIR/bin/applywarp \
- -i $odir/${s}_avgtsnr \
- -r src/tnt/templates/grpbold3Tp2/brain.nii.gz \
- -o $odir/${s}_avgtsnr_grpbold3Tp2 \
- -w src/tnt/${s}/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz \
- --interp=trilinear
- done
- $FSLDIR/bin/fslmerge -t $odir/alltsnr_grpbold3Tp2 $odir/*_avgtsnr_grpbold3Tp2.nii.gz
- $FSLDIR/bin/fslmaths $odir/alltsnr_grpbold3Tp2 -Tmean $odir/avgtsnr_grpbold3Tp2
- $FSLDIR/bin/fslmaths $odir/alltsnr_grpbold3Tp2 -Tstd $odir/stdtsnr_grpbold3Tp2
- $FSLDIR/bin/fslmaths $odir/avgtsnr_grpbold3Tp2 -uthr 60 -bin $odir/avgtsnr_grpbold3Tp2_lt60
- $FSLDIR/bin/fslmaths $odir/avgtsnr_grpbold3Tp2 -uthr 50 -bin $odir/avgtsnr_grpbold3Tp2_lt50
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