FSL系列教程 #5. FSL脚本编写

#!/bin/bash

# Generate the subject list to make modifying this script
# to run just a subset of subjects easier.

# 依次遍历26个被试数据
for id in `seq -w 1 26` ; do
    subj="sub-$id"
    echo "===> Starting processing of $subj"
    echo
    cd $subj


        # 颅骨去除
        # If the brain mask doesn’t exist, create it
        if [ ! -f anat/${subj}_T1w_brain_f02.nii.gz ]; then
            echo "Skull-stripped brain not found, using bet with a fractional intensity threshold of 0.2"
            # Note: This fractional intensity appears to work well for most of the subjects in the
            # Flanker dataset. You may want to change it if you modify this script for your own study.
            bet2 anat/${subj}_T1w.nii.gz \
                anat/${subj}_T1w_brain_f02.nii.gz -f 0.2
        fi

        # Copy the design files into the subject directory, and then
        # change “sub-08” to the current subject number
        cp ../design_run1.fsf .
        cp ../design_run2.fsf .

        # 替换*.fsf中的"sub-08"为当前需要处理的被试名称
        # Note that we are using the | character to delimit the patterns
        # instead of the usual / character because there are / characters
        # in the pattern.
        sed -i '' "s|sub-08|${subj}|g" \
            design_run1.fsf
        sed -i '' "s|sub-08|${subj}|g" \
            design_run2.fsf


        # 直接使用feat执行*.fsf脚本
        # Usage: feat <design.fsf>
        # Now everything is set up to run feat
        echo "===> Starting feat for run 1"
        feat design_run1.fsf
        echo "===> Starting feat for run 2"
        feat design_run2.fsf
                echo

    # Go back to the directory containing all of the subjects, and repeat the loop
    cd ..
done

echo