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- #!/bin/bash
- set -e
- set -u
- corrtype=$1
- odir="qa/bold3Tp2/aoav_corr_${corrtype}"
- mkdir -p $odir
- for s in sub-*; do
- if [ "$s" = "sub-10" ]; then
- # this subject doesn't have usable 7T data
- continue
- fi
- echo "$s"
- $FSLDIR/bin/fslmerge -t $odir/${s}_all $s/in_bold3Tp2/${s}_*_${corrtype}Z.nii.gz
- $FSLDIR/bin/fslmaths $odir/${s}_all -Tmean $odir/${s}_avg
- $FSLDIR/bin/applywarp \
- -i $odir/${s}_avg \
- -r src/tnt/templates/grpbold3Tp2/brain.nii.gz \
- -o $odir/${s}_avg_grpbold3Tp2 \
- -w src/tnt/${s}/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz \
- --interp=trilinear
- $FSLDIR/bin/flirt \
- -in src/tnt/${s}/bold7Tp1/brain_mask.nii.gz \
- -ref src/tnt/${s}/bold3Tp2/brain.nii.gz \
- -init src/tnt/${s}/bold7Tp1/in_bold3Tp2/xfm_6dof.mat \
- -applyxfm \
- -o $odir/${s}_brain_mask_in3T \
- -interp nearestneighbour
- $FSLDIR/bin/applywarp \
- -i $odir/${s}_brain_mask_in3T \
- -r src/tnt/templates/grpbold3Tp2/brain.nii.gz \
- -o $odir/${s}_brain_mask \
- -w src/tnt/${s}/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz \
- --interp=nn
- done
- $FSLDIR/bin/fslmerge -t $odir/allmask_grpbold3Tp2 $odir/*_brain_mask.nii.gz
- $FSLDIR/bin/fslmaths $odir/allmask_grpbold3Tp2 -Tmean -thr 1 -bin $odir/mask_grpbold3Tp2
- $FSLDIR/bin/fslmerge -t $odir/all_grpbold3Tp2 $odir/*_avg_grpbold3Tp2.nii.gz
- $FSLDIR/bin/fslmaths $odir/all_grpbold3Tp2 -Tmean $odir/avg_grpbold3Tp2
- $FSLDIR/bin/fslmaths $odir/all_grpbold3Tp2 -Tstd $odir/std_grpbold3Tp2
- cd $odir
- $FSLDIR/bin/easythresh avg_grpbold3Tp2.nii.gz mask_grpbold3Tp2 3.1 0.05 \
- ../../../src/tnt/templates/grpbold3Tp2/brain.nii.gz easythresh_31_05
- $FSLDIR/bin/easythresh avg_grpbold3Tp2.nii.gz mask_grpbold3Tp2 2.3 0.05 \
- ../../../src/tnt/templates/grpbold3Tp2/brain.nii.gz easythresh_23_05
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