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@@ -0,0 +1,26 @@
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+#!/bin/bash
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+
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+set -e
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+set -u
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+
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+odir="qa/tsnr/bold3Tp2"
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+mkdir -p $odir
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+
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+for s in sub-*; do
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+ echo "$s"
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+ $FSLDIR/bin/fslmerge -t $odir/${s}_alltsnr $s/in_bold3Tp2/${s}_*_bold_tsnr.nii.gz
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+ $FSLDIR/bin/fslmaths $odir/${s}_alltsnr -Tmean $odir/${s}_avgtsnr
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+ $FSLDIR/bin/applywarp \
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+ -i $odir/${s}_avgtsnr \
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+ -r src/tnt/templates/grpbold3Tp2/brain.nii.gz \
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+ -o $odir/${s}_avgtsnr_grpbold3Tp2 \
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+ -w src/tnt/${s}/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz \
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+ --interp=trilinear
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+done
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+
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+$FSLDIR/bin/fslmerge -t $odir/alltsnr_grpbold3Tp2 $odir/*_avgtsnr_grpbold3Tp2.nii.gz
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+$FSLDIR/bin/fslmaths $odir/alltsnr_grpbold3Tp2 -Tmean $odir/avgtsnr_grpbold3Tp2
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+$FSLDIR/bin/fslmaths $odir/alltsnr_grpbold3Tp2 -Tstd $odir/stdtsnr_grpbold3Tp2
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+$FSLDIR/bin/fslmaths $odir/avgtsnr_grpbold3Tp2 -uthr 60 -bin $odir/avgtsnr_grpbold3Tp2_lt60
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+$FSLDIR/bin/fslmaths $odir/avgtsnr_grpbold3Tp2 -uthr 50 -bin $odir/avgtsnr_grpbold3Tp2_lt50
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+
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